Genetic Variant NM_001396956.1:c.1641T>C (chr15-22465901-T-C) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001396956.1(GOLGA6L22):c.1641T>C(p.His547His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000070 ( 0 hom., cov: 5)

Exomes 𝑓: 0.0000048 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L22
NM_001396956.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0350

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: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.1).

BP6

Variant 15-22465901-T-C is Benign according to our data. Variant chr15-22465901-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3770742.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.035 with no splicing effect.

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.1641T>C	p.His547His	synonymous	Exon 8 of 9	NP_001383885.1	H0YM25
	GOLGA6L22	NM_001396957.1		c.1638T>C	p.His546His	synonymous	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.1641T>C	p.His547His	synonymous	Exon 8 of 9	ENSP00000483673.2	H0YM25
	ENSG00000310081	ENST00000846990.1		n.151+4510A>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0000696

AC:

AN:

43078

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000923

Gnomad FIN

AF:

0.000435

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000387

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000948

AC:

AN:

137076

AF XY:

0.0000823

show subpopulations

Gnomad AFR exome

AF:

0.000176

Gnomad AMR exome

AF:

0.0000447

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000207

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000754

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000481

AC:

AN:

1039782

Hom.:

Cov.:

AF XY:

0.00000770

AC XY:

AN XY:

519164

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

15158

American (AMR)

AF:

0.00

AC:

AN:

28398

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17418

East Asian (EAS)

AF:

0.00

AC:

AN:

23758

South Asian (SAS)

AF:

0.0000156

AC:

AN:

64202

European-Finnish (FIN)

AF:

0.00

AC:

AN:

41652

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2566

European-Non Finnish (NFE)

AF:

0.00000496

AC:

AN:

806000

Other (OTH)

AF:

0.00

AC:

AN:

40630

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.415

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.0000696

AC:

AN:

43110

Hom.:

Cov.:

AF XY:

0.0000977

AC XY:

AN XY:

20468

show subpopulations

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

African (AFR)

AF:

0.00

AC:

AN:

6810

American (AMR)

AF:

0.00

AC:

AN:

3434

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1256

East Asian (EAS)

AF:

0.00

AC:

AN:

1568

South Asian (SAS)

AF:

0.000926

AC:

AN:

1080

European-Finnish (FIN)

AF:

0.000435

AC:

AN:

2300

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0000387

AC:

AN:

25850

Other (OTH)

AF:

0.00

AC:

AN:

572

⚠️ 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:

0.000503

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_noAF

Benign

-1.1

CADD

Benign

1.3

(source)

DANN

Benign

0.33

PhyloP100

-0.035

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

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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