3-148663735-T-C

Variant names:

• chr3-148663735-T-C
• rs2087737

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 0.516 in 151,888 control chromosomes in the GnomAD database, including 23,201 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 0.52 (23201 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 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: 0.516 AC: 78350 AN: 151770 Hom.: 23187 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.516 AC: 78386 AN: 151888 Hom.: 23201 Cov.: 32 AF XY: 0.523 AC XY: 38802 AN XY: 74236

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.528

Alfa AF: 0.496 Hom.: 2739

Bravo AF: 0.509

Asia WGS AF: 0.633 AC: 2200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2087737; hg19: chr3-148381522;