chr3-68702839-C-T

Variant names:

• chr3-68702839-C-T
• rs4538379

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 0.642 in 151,992 control chromosomes in the GnomAD database, including 31,981 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 0.64 (31981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888

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 = 0.898 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: 0.642 AC: 97572 AN: 151874 Hom.: 31978 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.642 AC: 97620 AN: 151992 Hom.: 31981 Cov.: 32 AF XY: 0.649 AC XY: 48166 AN XY: 74270

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.637

Alfa AF: 0.635 Hom.: 3878

Bravo AF: 0.626

Asia WGS AF: 0.800 AC: 2782 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	0.18
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4538379; hg19: chr3-68751990;