rs2960420

chr3-12273013-C-G

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 0.407 in 152,020 control chromosomes in the GnomAD database, including 13,143 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 0.41 (13143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.543 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: 0.407 AC: 61792 AN: 151904 Hom.: 13122 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.407 AC: 61855 AN: 152020 Hom.: 13143 Cov.: 32 AF XY: 0.409 AC XY: 30372 AN XY: 74292

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.384

Alfa AF: 0.376 Hom.: 1543

Bravo AF: 0.403

Asia WGS AF: 0.496 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.25
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2960420; hg19: chr3-12314512;