rs2987763

Variant names:

• chr1-153313558-T-A
• rs2987763

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 0.411 in 152,060 control chromosomes in the GnomAD database, including 13,379 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 0.41 (13379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 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: 0.411 AC: 62470 AN: 151942 Hom.: 13374 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.411 AC: 62506 AN: 152060 Hom.: 13379 Cov.: 32 AF XY: 0.406 AC XY: 30191 AN XY: 74332

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.399

Alfa AF: 0.446 Hom.: 1938

Bravo AF: 0.401

Asia WGS AF: 0.237 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.59
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2987763; hg19: chr1-153286034;