rs3934658

chr12-121599194-A-Cchr12-121599194-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;