3-42238461-T-C

Position:

• chr3-42238461-T-C

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/exons	MANE	UniProt

Ensembl

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