rs2501787

chr1-17304232-T-C

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 0.62 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.619

Alfa AF: 0.618 Hom.: 2719

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2501787; hg19: chr1-17630727;