rs2501787

Variant names:

• chr1-17304232-T-C
• rs2501787

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 0.62 in 152,018 control chromosomes in the GnomAD database, including 30,085 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 0.62 (30085 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 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: 0.620 AC: 94113 AN: 151900 Hom.: 30025 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.620 AC: 94240 AN: 152018 Hom.: 30085 Cov.: 32 AF XY: 0.616 AC XY: 45809 AN XY: 74314

African (AFR) AF: 0.766 AC: 31781 AN: 41470

American (AMR) AF: 0.581 AC: 8887 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1627 AN: 3466

East Asian (EAS) AF: 0.362 AC: 1870 AN: 5162

South Asian (SAS) AF: 0.532 AC: 2567 AN: 4822

European-Finnish (FIN) AF: 0.566 AC: 5983 AN: 10566

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39450 AN: 67932

Other (OTH) AF: 0.619 AC: 1309 AN: 2114

Alfa AF: 0.586 Hom.: 13486

Bravo AF: 0.626

Asia WGS AF: 0.525 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.56
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2501787; hg19: chr1-17630727;