rs3951042

Variant names:

• chr6-118401332-C-T
• rs3951042

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 0.464 in 152,084 control chromosomes in the GnomAD database, including 16,864 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 0.46 (16864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 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: 0.464 AC: 70567 AN: 151966 Hom.: 16866 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.464 AC: 70589 AN: 152084 Hom.: 16864 Cov.: 32 AF XY: 0.460 AC XY: 34165 AN XY: 74350

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.435

Alfa AF: 0.497 Hom.: 2478

Bravo AF: 0.445

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.10
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3951042; hg19: chr6-118722495; COSMIC: COSV69422204;