rs2502807

Variant names:

• chr1-161247903-C-A
• rs2502807

Your query was ambiguous. Multiple possible variants found:

• chr1-161247903-C-A
• chr1-161247903-C-G
• chr1-161247903-C-T

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 0.704 in 152,190 control chromosomes in the GnomAD database, including 38,692 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 0.70 (38692 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.916
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 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: 0.704 AC: 106994 AN: 152072 Hom.: 38636 Cov.: 34

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.704 AC: 107105 AN: 152190 Hom.: 38692 Cov.: 34 AF XY: 0.706 AC XY: 52497 AN XY: 74390

African (AFR) AF: 0.844 AC: 35032 AN: 41522

American (AMR) AF: 0.748 AC: 11431 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2134 AN: 3468

East Asian (EAS) AF: 0.943 AC: 4894 AN: 5188

South Asian (SAS) AF: 0.695 AC: 3357 AN: 4828

European-Finnish (FIN) AF: 0.630 AC: 6665 AN: 10572

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41374 AN: 67998

Other (OTH) AF: 0.690 AC: 1460 AN: 2116

Alfa AF: 0.652 Hom.: 27326

Bravo AF: 0.722

Asia WGS AF: 0.833 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.0
DANN	Benign	0.65
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs2502807; hg19: chr1-161217693;