3-42238461-T-C

Variant names:

• chr3-42238461-T-C
• rs6791019

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.552 AC: 22872 AN: 41418

American (AMR) AF: 0.375 AC: 5726 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 685 AN: 3462

East Asian (EAS) AF: 0.736 AC: 3800 AN: 5162

South Asian (SAS) AF: 0.286 AC: 1376 AN: 4814

European-Finnish (FIN) AF: 0.309 AC: 3261 AN: 10544

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15876 AN: 67960

Other (OTH) AF: 0.327 AC: 689 AN: 2106

Alfa AF: 0.281 Hom.: 18728

Bravo AF: 0.377

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.49
DANN	Benign	0.55
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs6791019; hg19: chr3-42279953;