Genetic Variant NM_001304388.2:c.1702T>C (chr15-23440773-A-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001304388.2(GOLGA6L2):c.1702T>C(p.Ser568Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S568A) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GOLGA6L2
NM_001304388.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.690

Publications

7 publications found

Variant links:

Genes affected

GOLGA6L2 (HGNC:26695): (golgin A6 family like 2) Predicted to be located in cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

GOLGA6L2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.08171812).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304388.2. 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
	GOLGA6L2	NM_001304388.2	MANE Select	c.1702T>C	p.Ser568Pro	missense	Exon 8 of 8	NP_001291317.1	Q8N9W4-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
GOLGA6L2	ENST00000567107.6	TSL:5 MANE Select	c.1702T>C	p.Ser568Pro	missense	Exon 8 of 8	ENSP00000454407.1	Q8N9W4-3
GOLGA6L2	ENST00000566571.5	TSL:5	n.*983T>C		non_coding_transcript_exon	Exon 7 of 7	ENSP00000456523.1	H3BS38
GOLGA6L2	ENST00000566571.5	TSL:5	n.*983T>C		3_prime_UTR	Exon 7 of 7	ENSP00000456523.1	H3BS38

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

36206

Hom.:

Cov.:

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:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1249488

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

619728

African (AFR)

AF:

0.00

AC:

AN:

27726

American (AMR)

AF:

0.00

AC:

AN:

32972

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23210

East Asian (EAS)

AF:

0.00

AC:

AN:

33348

South Asian (SAS)

AF:

0.00

AC:

AN:

73244

European-Finnish (FIN)

AF:

0.00

AC:

AN:

41288

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5336

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

959836

Other (OTH)

AF:

0.00

AC:

AN:

52528

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

36244

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

17438

African (AFR)

AF:

0.00

AC:

AN:

11042

American (AMR)

AF:

0.00

AC:

AN:

3772

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

834

East Asian (EAS)

AF:

0.00

AC:

AN:

940

South Asian (SAS)

AF:

0.00

AC:

AN:

840

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2172

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

15812

Other (OTH)

AF:

0.00

AC:

AN:

516

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Benign

-0.44

CADD

Benign

6.4

(source)

DANN

Benign

0.62

FATHMM_MKL

Benign

0.00094

LIST_S2

Benign

0.28

M_CAP

Benign

0.011

MetaRNN

Benign

0.082

PhyloP100

0.69

PROVEAN

Benign

0.14

Sift4G

Benign

0.38

Vest4

0.11

MVP

0.40

MPC

0.014

Varity_R

0.10

gMVP

0.015

Mutation Taster

=100/0

polymorphism

(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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over