rs4319601

Variant names:

• chr13-30772985-T-C
• rs4319601

Variant summary

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

The variant allele was found at a frequency of 0.523 in 151,852 control chromosomes in the GnomAD database, including 23,244 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 0.52 (23244 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 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

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79355 AN: 151734 Hom.: 23235 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.523 AC: 79388 AN: 151852 Hom.: 23244 Cov.: 31 AF XY: 0.532 AC XY: 39464 AN XY: 74208

African (AFR) AF: 0.232 AC: 9598 AN: 41372

American (AMR) AF: 0.655 AC: 9995 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2047 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2919 AN: 5156

South Asian (SAS) AF: 0.564 AC: 2704 AN: 4794

European-Finnish (FIN) AF: 0.691 AC: 7287 AN: 10550

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42928 AN: 67946

Other (OTH) AF: 0.567 AC: 1196 AN: 2108

Alfa AF: 0.571 Hom.: 3288

Bravo AF: 0.509

Asia WGS AF: 0.563 AC: 1959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.61
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4319601; hg19: chr13-31347122; COSMIC: COSV69345910;