rs2501870

Variant names:

• chr1-161242779-G-A
• rs2501870

Your query was ambiguous. Multiple possible variants found:

• chr1-161242779-G-A
• chr1-161242779-G-C
• chr1-161242779-G-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 0.29 in 151,912 control chromosomes in the GnomAD database, including 6,488 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 0.29 (6488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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: 0.290 AC: 44066 AN: 151794 Hom.: 6482 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.290 AC: 44105 AN: 151912 Hom.: 6488 Cov.: 32 AF XY: 0.293 AC XY: 21740 AN XY: 74286

African (AFR) AF: 0.312 AC: 12915 AN: 41396

American (AMR) AF: 0.317 AC: 4830 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 952 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1689 AN: 5170

South Asian (SAS) AF: 0.303 AC: 1462 AN: 4820

European-Finnish (FIN) AF: 0.318 AC: 3351 AN: 10540

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17924 AN: 67944

Other (OTH) AF: 0.296 AC: 625 AN: 2114

Alfa AF: 0.271 Hom.: 16882

Bravo AF: 0.297

Asia WGS AF: 0.329 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.6
DANN	Benign	0.73
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs2501870; hg19: chr1-161212569;