3-42238461-T-C

Variant names:

• chr3-42238461-T-C
• rs6791019

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 0.359 in 151,938 control chromosomes in the GnomAD database, including 11,621 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 0.36 (11621 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989

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 (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.359 AC: 54443 AN: 151820 Hom.: 11592 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.359 AC: 54529 AN: 151938 Hom.: 11621 Cov.: 32 AF XY: 0.363 AC XY: 26959 AN XY: 74264

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.327

Alfa AF: 0.258 Hom.: 9329

Bravo AF: 0.377

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.49
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: rs6791019; hg19: chr3-42279953;