rs2713594

Positions:

• chr3-128477657-G-A

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 0.472 in 152,010 control chromosomes in the GnomAD database, including 17,395 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 0.47 (17395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71626 AN: 151892 Hom.: 17373 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.472 AC: 71697 AN: 152010 Hom.: 17395 Cov.: 32 AF XY: 0.472 AC XY: 35028 AN XY: 74284

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.464

Alfa AF: 0.436 Hom.: 20532

Bravo AF: 0.480

Asia WGS AF: 0.510 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.87
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2713594; hg19: chr3-128196500;