rs974515

Variant names:

• chr3-3462176-C-T
• rs974515
• ENST00000420000.6:n.201-79526G>A

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.201-79526G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,788 control chromosomes in the GnomAD database, including 14,083 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 0.40 (14083 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 4 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223727	ENST00000420000.6	n.201-79526G>A		intron_variant	Intron 2 of 4	4
ENSG00000223727	ENST00000451031.5	n.78-21171G>A		intron_variant	Intron 1 of 5	3
ENSG00000223727	ENST00000455703.1	n.59+21863G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59939 AN: 151670 Hom.: 14073 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.395 AC: 60005 AN: 151788 Hom.: 14083 Cov.: 32 AF XY: 0.396 AC XY: 29400 AN XY: 74166

African (AFR) AF: 0.613 AC: 25376 AN: 41386

American (AMR) AF: 0.332 AC: 5067 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 872 AN: 3470

East Asian (EAS) AF: 0.821 AC: 4222 AN: 5140

South Asian (SAS) AF: 0.377 AC: 1808 AN: 4802

European-Finnish (FIN) AF: 0.266 AC: 2799 AN: 10504

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18850 AN: 67930

Other (OTH) AF: 0.361 AC: 761 AN: 2108

Alfa AF: 0.347 Hom.: 1404

Bravo AF: 0.411

Asia WGS AF: 0.570 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.7
DANN	Benign	0.76
PhyloP100		-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs974515; hg19: chr3-3503860;