3-87061524-T-C

Variant names:

• chr3-87061524-T-C
• rs2660753

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 0.761 in 152,054 control chromosomes in the GnomAD database, including 46,501 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 0.76 (46501 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.882 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: 0.761 AC: 115690 AN: 151936 Hom.: 46491 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.761 AC: 115728 AN: 152054 Hom.: 46501 Cov.: 31 AF XY: 0.762 AC XY: 56658 AN XY: 74324

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.777

Alfa AF: 0.860 Hom.: 129035

Bravo AF: 0.741

Asia WGS AF: 0.717 AC: 2494 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2660753; hg19: chr3-87110674;