rs7295581

Variant names:

• chr12-4710935-A-G
• rs7295581
• ENST00000648836.1:c.963+25610A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648836.1(ENSG00000255639):​c.963+25610A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,106 control chromosomes in the GnomAD database, including 2,761 homozygotes. 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: 𝑓 0.19 (2761 hom., cov: 32)
• Consequence: ENSG00000255639 ENST00000648836.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 2 publications found

Genes affected

ENSG00000255639 (HGNC:):

GAU1 (HGNC:53880): (GALNT8 antisense upstream 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648836.1. 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
	GAU1	NR_110112.1		n.239-6638T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255639	ENST00000648836.1		c.963+25610A>G		intron	N/A	ENSP00000497305.1	A0A3B3ISG8
	GAU1	ENST00000527518.1	TSL:1	n.239-6638T>C		intron	N/A
	ENSG00000255639	ENST00000543979.1	TSL:2	n.590-15597A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28352 AN: 151988 Hom.: 2762 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.199

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.187 AC: 28372 AN: 152106 Hom.: 2761 Cov.: 32 AF XY: 0.185 AC XY: 13765 AN XY: 74376

African (AFR) AF: 0.214 AC: 8886 AN: 41466

American (AMR) AF: 0.141 AC: 2163 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3466

East Asian (EAS) AF: 0.0314 AC: 163 AN: 5186

South Asian (SAS) AF: 0.128 AC: 617 AN: 4808

European-Finnish (FIN) AF: 0.198 AC: 2099 AN: 10588

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13345 AN: 67982

Other (OTH) AF: 0.196 AC: 415 AN: 2114

Alfa AF: 0.188 Hom.: 921

Bravo AF: 0.182

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.33
PhyloP100		0.45

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7295581;

hg19: chr12-4820101;