rs3951042

Positions:

• chr6-118401332-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 0.464 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;