rs763318

Variant names:

• chr4-12961950-G-A
• rs763318
• ENST00000789800.1:n.120+10982C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-12961950-G-A
• chr4-12961950-G-C
• chr4-12961950-G-T

Variant summary

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

The ENST00000789800.1(ENSG00000302819):​n.120+10982C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,908 control chromosomes in the GnomAD database, including 19,583 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 0.50 (19583 hom., cov: 32)
• Consequence: ENSG00000302819 ENST00000789800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 18 publications found

Genes affected

ENSG00000302819 (HGNC:):

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 = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789800.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302819	ENST00000789800.1		n.120+10982C>T		intron	N/A
	ENSG00000302819	ENST00000789802.1		n.114-72C>T		intron	N/A
	ENSG00000302819	ENST00000789803.1		n.397-72C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76445 AN: 151788 Hom.: 19556 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.504 AC: 76519 AN: 151908 Hom.: 19583 Cov.: 32 AF XY: 0.505 AC XY: 37494 AN XY: 74254

African (AFR) AF: 0.594 AC: 24631 AN: 41438

American (AMR) AF: 0.463 AC: 7045 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3472

East Asian (EAS) AF: 0.493 AC: 2541 AN: 5156

South Asian (SAS) AF: 0.584 AC: 2812 AN: 4816

European-Finnish (FIN) AF: 0.506 AC: 5337 AN: 10552

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31132 AN: 67930

Other (OTH) AF: 0.464 AC: 981 AN: 2112

Alfa AF: 0.468 Hom.: 80340

Bravo AF: 0.497

Asia WGS AF: 0.586 AC: 2038 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	1.1
DANN	Benign	0.71
PhyloP100		-0.061

Splicing

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: rs763318;

hg19: chr4-12963574;