rs3912607

chr3-162780970-C-T

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 0.439 in 151,290 control chromosomes in the GnomAD database, including 14,878 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 0.44 (14878 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 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: 0.439 AC: 66390 AN: 151172 Hom.: 14868 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.439 AC: 66429 AN: 151290 Hom.: 14878 Cov.: 31 AF XY: 0.444 AC XY: 32849 AN XY: 73934

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.413

Alfa AF: 0.443 Hom.: 6543

Bravo AF: 0.425

Asia WGS AF: 0.287 AC: 998 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.31
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3912607; hg19: chr3-162498758;