rs4765780

Variant names:

• chr12-4714793-G-A
• rs4765780
• ENST00000648836.1:c.963+29468G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-4714793-G-A
• chr12-4714793-G-C

Variant summary

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

The ENST00000648836.1(ENSG00000255639):​c.963+29468G>A 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 151,980 control chromosomes in the GnomAD database, including 17,074 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 (17074 hom., cov: 31)
• Consequence: ENSG00000255639 ENST00000648836.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAU1	NR_110112.1		n.238+5072C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255639	ENST00000648836.1		c.963+29468G>A		intron	N/A	ENSP00000497305.1
	GAU1	ENST00000527518.1	TSL:1	n.238+5072C>T		intron	N/A
	ENSG00000255639	ENST00000543979.1	TSL:2	n.590-11739G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71368 AN: 151862 Hom.: 17070 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.470 AC: 71410 AN: 151980 Hom.: 17074 Cov.: 31 AF XY: 0.465 AC XY: 34574 AN XY: 74280

African (AFR) AF: 0.426 AC: 17648 AN: 41440

American (AMR) AF: 0.493 AC: 7528 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1869 AN: 5162

South Asian (SAS) AF: 0.294 AC: 1419 AN: 4820

European-Finnish (FIN) AF: 0.491 AC: 5177 AN: 10544

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34656 AN: 67964

Other (OTH) AF: 0.437 AC: 921 AN: 2106

Alfa AF: 0.472 Hom.: 2147

Bravo AF: 0.473

Asia WGS AF: 0.311 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.14

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: rs4765780; hg19: chr12-4823959;