rs4766282

Variant names:

• chr12-4715704-A-G
• rs4766282
• ENST00000648836.1:c.963+30379A>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+30379A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,016 control chromosomes in the GnomAD database, including 17,076 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 0.47 (17076 hom., cov: 32)
• Consequence: ENSG00000255639 ENST00000648836.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAU1	NR_110112.1	n.238+4161T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255639	ENST00000648836.1	c.963+30379A>G		intron_variant	Intron 10 of 14			ENSP00000497305.1
GAU1	ENST00000527518.1	n.238+4161T>C		intron_variant	Intron 1 of 3	1
ENSG00000255639	ENST00000543979.1	n.590-10828A>G		intron_variant	Intron 5 of 5	2
ENSG00000255639	ENST00000544741.2	n.241-10828A>G		intron_variant	Intron 3 of 5	3		ENSP00000456318.2

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71413 AN: 151896 Hom.: 17072 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.470 AC: 71455 AN: 152016 Hom.: 17076 Cov.: 32 AF XY: 0.466 AC XY: 34585 AN XY: 74282

African (AFR) AF: 0.427 AC: 17696 AN: 41464

American (AMR) AF: 0.493 AC: 7537 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1534 AN: 3464

East Asian (EAS) AF: 0.362 AC: 1876 AN: 5176

South Asian (SAS) AF: 0.294 AC: 1422 AN: 4830

European-Finnish (FIN) AF: 0.490 AC: 5166 AN: 10544

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.510 AC: 34646 AN: 67940

Other (OTH) AF: 0.437 AC: 923 AN: 2110

Alfa AF: 0.479 Hom.: 2260

Bravo AF: 0.474

Asia WGS AF: 0.310 AC: 1083 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.094
DANN	Benign	0.47
PhyloP100		-1.1

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: rs4766282; hg19: chr12-4824870;