rs4319601

Variant names:

• chr13-30772985-T-C
• rs4319601

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.567

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

Splicing

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

Publications

LitVar

Other links and lift over

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