3-101135338-C-G

Position:

• chr3-101135338-C-G

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 0.683 in 151,778 control chromosomes in the GnomAD database, including 35,841 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 0.68 (35841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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: 0.683 AC: 103524 AN: 151660 Hom.: 35775 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.683 AC: 103650 AN: 151778 Hom.: 35841 Cov.: 32 AF XY: 0.687 AC XY: 50953 AN XY: 74154

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.665

Alfa AF: 0.536 Hom.: 1478

Bravo AF: 0.690

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1911573; hg19: chr3-100854182;