rs2987763

Variant names:

• chr1-153313558-T-A
• rs2987763

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.356 AC: 14778 AN: 41478

American (AMR) AF: 0.349 AC: 5338 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1454 AN: 3470

East Asian (EAS) AF: 0.191 AC: 985 AN: 5148

South Asian (SAS) AF: 0.269 AC: 1296 AN: 4826

European-Finnish (FIN) AF: 0.489 AC: 5167 AN: 10568

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.472 AC: 32072 AN: 67964

Other (OTH) AF: 0.399 AC: 842 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.59
DANN	Benign	0.51
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2987763; hg19: chr1-153286034;