15-23129898-A-G

Variant names:

• chr15-23129898-A-G
• rs1374626047
• NM_001001413.3:c.1555T>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001001413.3(GOLGA6L1):​c.1555T>C​(p.Trp519Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 6/8 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0015 (0 hom., cov: 34)
  • Exomes 𝑓: 0.00024 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L1 NM_001001413.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

Genes affected

GOLGA6L1 (HGNC:37444): (golgin A6 family like 1)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.06880534).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA6L1	NM_001001413.3	c.1555T>C	p.Trp519Arg	missense_variant	Exon 8 of 9	ENST00000614055.2	NP_001001413.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA6L1	ENST00000614055.2	c.1555T>C	p.Trp519Arg	missense_variant	Exon 8 of 9	5	NM_001001413.3	ENSP00000478478.1

Frequencies

GnomAD3 genomes AF: 0.00148 AC: 166 AN: 112030 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.00145

Gnomad AMI AF: 0.00168

Gnomad AMR AF: 0.00129

Gnomad ASJ AF: 0.00108

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.00193

Gnomad FIN AF: 0.00204

Gnomad MID AF: 0.00658

Gnomad NFE AF: 0.00144

Gnomad OTH AF: 0.00131

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000240 AC: 181 AN: 753020 Hom.: 0 Cov.: 19 AF XY: 0.000285 AC XY: 111 AN XY: 389850

Gnomad4 AFR exome AF: 0.0000466

Gnomad4 AMR exome AF: 0.000458

Gnomad4 ASJ exome AF: 0.000102

Gnomad4 EAS exome AF: 0.00152

Gnomad4 SAS exome AF: 0.000449

Gnomad4 FIN exome AF: 0.0000451

Gnomad4 NFE exome AF: 0.000161

Gnomad4 OTH exome AF: 0.000255

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00147 AC: 165 AN: 112184 Hom.: 0 Cov.: 34 AF XY: 0.00151 AC XY: 83 AN XY: 54966

Gnomad4 AFR AF: 0.00144

Gnomad4 AMR AF: 0.00129

Gnomad4 ASJ AF: 0.00108

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.00160

Gnomad4 FIN AF: 0.00204

Gnomad4 NFE AF: 0.00144

Gnomad4 OTH AF: 0.00129

Alfa AF: 0.000421 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
CADD	Benign	5.4
DANN	Benign	0.32
LIST_S2	Benign	0.021	T
MetaRNN	Benign	0.069	T
Sift4G	Benign	0.41	T
Vest4		0.11
gMVP		0.015

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

Other links and lift over

dbSNP: rs1374626047; hg19: -;