15-20534333-G-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7

The NM_001145004.2(GOLGA6L6):​c.2101C>A​(p.Arg701Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 16)
Exomes 𝑓: 0.000024 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

GOLGA6L6
NM_001145004.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.78
Variant links:
Genes affected
GOLGA6L6 (HGNC:37225): (golgin A6 family like 6)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=-5.78 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GOLGA6L6NM_001145004.2 linkc.2101C>A p.Arg701Arg synonymous_variant Exon 8 of 9 ENST00000619213.1 NP_001138476.2 A8MZA4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GOLGA6L6ENST00000619213.1 linkc.2101C>A p.Arg701Arg synonymous_variant Exon 8 of 9 5 NM_001145004.2 ENSP00000480376.1 A8MZA4

Frequencies

GnomAD3 genomes
Cov.:
16
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000240
AC:
28
AN:
1165724
Hom.:
0
Cov.:
25
AF XY:
0.0000292
AC XY:
17
AN XY:
582386
show subpopulations
Gnomad4 AFR exome
AF:
0.0000381
Gnomad4 AMR exome
AF:
0.0000288
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000272
Gnomad4 OTH exome
AF:
0.0000395
GnomAD4 genome
Cov.:
16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.4
DANN
Benign
0.24

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1303583214; hg19: chr15-20739571; API