chr4-12961950-G-A

Variant names:

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374493	XR_001741369.2	n.99+10982C>T		intron_variant	Intron 1 of 2
LOC105374493	XR_001741370.2	n.94+10987C>T		intron_variant	Intron 1 of 2
LOC105374493	XR_007058044.1	n.11630+1726C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302819	ENST00000789800.1	n.120+10982C>T		intron_variant	Intron 1 of 1
ENSG00000302819	ENST00000789802.1	n.114-72C>T		intron_variant	Intron 1 of 1
ENSG00000302819	ENST00000789803.1	n.397-72C>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs763318; hg19: chr4-12963574;