chr3-138135633-A-G

Position:

• chr3-138135633-A-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 0.544 in 152,046 control chromosomes in the GnomAD database, including 25,003 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 0.54 (25003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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: 0.544 AC: 82640 AN: 151928 Hom.: 25002 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.544 AC: 82661 AN: 152046 Hom.: 25003 Cov.: 32 AF XY: 0.546 AC XY: 40595 AN XY: 74308

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.583

Alfa AF: 0.450 Hom.: 1347

Bravo AF: 0.532

Asia WGS AF: 0.534 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2346747; hg19: chr3-137854475;