chr3-87040015-G-A

Position:

• chr3-87040015-G-A

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 0.606 in 151,984 control chromosomes in the GnomAD database, including 28,561 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 0.61 (28561 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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: 0.606 AC: 92058 AN: 151866 Hom.: 28544 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.606 AC: 92122 AN: 151984 Hom.: 28561 Cov.: 33 AF XY: 0.611 AC XY: 45387 AN XY: 74288

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.601

Alfa AF: 0.628 Hom.: 5246

Bravo AF: 0.598

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.88
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1370041; hg19: chr3-87089165;