Genetic Variant GOLGA6L22:p.Glu466* (chr15-22465656-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001396956.1(GOLGA6L22):c.1396G>T(p.Glu466*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., cov: 6)

Exomes 𝑓: 0.0021 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L22
NM_001396956.1 stop_gained

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.82

Publications

0 publications found

Variant links:

Genes affected

GOLGA6L22 (HGNC:50289): (golgin A6 family like 22)

GOLGA6L22 links:

ENSG00000310081 (HGNC:):

ENSG00000310081 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP6

Variant 15-22465656-G-T is Benign according to our data. Variant chr15-22465656-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2644965.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396956.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L22	NM_001396956.1	MANE Select	c.1396G>T	p.Glu466*	stop_gained	Exon 8 of 9	NP_001383885.1	H0YM25
	GOLGA6L22	NM_001396957.1		c.1393G>T	p.Glu465*	stop_gained	Exon 8 of 9	NP_001383886.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L22	ENST00000622895.2	TSL:5 MANE Select	c.1396G>T	p.Glu466*	stop_gained	Exon 8 of 9	ENSP00000483673.2	H0YM25
	ENSG00000310081	ENST00000846990.1		n.151+4755C>A		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.000163

AC:

AN:

36828

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000163

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000228

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000651

AC:

AN:

153556

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00214

AC:

1688

AN:

788654

Hom.:

Cov.:

AF XY:

0.00228

AC XY:

922

AN XY:

403688

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00325

AC:

AN:

15090

American (AMR)

AF:

0.00212

AC:

AN:

29650

Ashkenazi Jewish (ASJ)

AF:

0.00500

AC:

AN:

16406

East Asian (EAS)

AF:

0.000193

AC:

AN:

31082

South Asian (SAS)

AF:

0.00537

AC:

319

AN:

59410

European-Finnish (FIN)

AF:

0.00113

AC:

AN:

36346

Middle Eastern (MID)

AF:

0.00416

AC:

AN:

2162

European-Non Finnish (NFE)

AF:

0.00181

AC:

1022

AN:

564416

Other (OTH)

AF:

0.00285

AC:

AN:

34092

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.298

Heterozygous variant carriers

142

283

425

566

708

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000163

AC:

AN:

36852

Hom.:

Cov.:

AF XY:

0.000172

AC XY:

AN XY:

17424

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000162

AC:

AN:

6158

American (AMR)

AF:

0.00

AC:

AN:

3040

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

988

East Asian (EAS)

AF:

0.00

AC:

AN:

1240

South Asian (SAS)

AF:

0.00

AC:

AN:

480

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2404

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000228

AC:

AN:

21924

Other (OTH)

AF:

0.00

AC:

AN:

404

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.242

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00320

Hom.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.25

BayesDel_noAF

Uncertain

0.12

CADD

Benign

(source)

DANN

Benign

0.97

Eigen

Uncertain

0.27

Eigen_PC

Benign

-0.12

FATHMM_MKL

Benign

0.0035

PhyloP100

-1.8

Vest4

0.043

Mutation Taster

=171/29

disease causing (fs/PTC)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over