rs3934658

Variant names:

• chr12-121599194-A-C
• rs3934658

Your query was ambiguous. Multiple possible variants found:

• chr12-121599194-A-C
• chr12-121599194-A-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 0.486 in 151,934 control chromosomes in the GnomAD database, including 18,847 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 0.49 (18847 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 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: 0.485 AC: 73669 AN: 151816 Hom.: 18788 Cov.: 31

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.486 AC: 73801 AN: 151934 Hom.: 18847 Cov.: 31 AF XY: 0.485 AC XY: 36017 AN XY: 74262

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.447

Alfa AF: 0.436 Hom.: 8871

Bravo AF: 0.494

Asia WGS AF: 0.520 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3934658; hg19: chr12-122037099;