NM_001001413.3:c.1555T>G

Variant names:

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

Variant summary

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

The NM_001001413.3(GOLGA6L1):​c.1555T>G​(p.Trp519Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 6/7 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. W519R) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., cov: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GOLGA6L1 NM_001001413.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=0.12164709).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001413.3. 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
	GOLGA6L1	NM_001001413.3	MANE Select	c.1555T>G	p.Trp519Gly	missense	Exon 8 of 9	NP_001001413.3	Q8N7Z2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA6L1	ENST00000614055.2	TSL:5 MANE Select	c.1555T>G	p.Trp519Gly	missense	Exon 8 of 9	ENSP00000478478.1	Q8N7Z2

Frequencies

GnomAD3 genomes AF: 0.00000891 AC: 1 AN: 112288 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000860

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: 0 AN: 753332 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 390000

African (AFR) AF: 0.00 AC: 0 AN: 21464

American (AMR) AF: 0.00 AC: 0 AN: 30578

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19576

East Asian (EAS) AF: 0.00 AC: 0 AN: 29090

South Asian (SAS) AF: 0.00 AC: 0 AN: 60152

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44364

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3552

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 509314

Other (OTH) AF: 0.00 AC: 0 AN: 35242

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000891 AC: 1 AN: 112288 Hom.: 0 Cov.: 34 AF XY: 0.0000182 AC XY: 1 AN XY: 54932

African (AFR) AF: 0.00 AC: 0 AN: 31134

American (AMR) AF: 0.0000860 AC: 1 AN: 11622

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2780

East Asian (EAS) AF: 0.00 AC: 0 AN: 3236

South Asian (SAS) AF: 0.00 AC: 0 AN: 3128

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7366

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 154

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 50728

Other (OTH) AF: 0.00 AC: 0 AN: 1538

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
CADD	Benign	13
DANN	Benign	0.28
LIST_S2	Benign	0.051	T
MetaRNN	Benign	0.12	T
PhyloP100		-2.9
Sift4G	Benign	0.44	T
Vest4		0.14
gMVP		0.014

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

Other links and lift over

dbSNP: rs1374626047;