rs2658997

Variant names:

• chr2-192206712-A-G
• rs2658997

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.272 in 152,060 control chromosomes in the GnomAD database, including 6,185 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 0.27 (6185 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 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: 0.272 AC: 41264 AN: 151942 Hom.: 6168 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.272 AC: 41330 AN: 152060 Hom.: 6185 Cov.: 32 AF XY: 0.270 AC XY: 20091 AN XY: 74340

African (AFR) AF: 0.400 AC: 16564 AN: 41446

American (AMR) AF: 0.277 AC: 4236 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 744 AN: 3470

East Asian (EAS) AF: 0.397 AC: 2051 AN: 5168

South Asian (SAS) AF: 0.199 AC: 959 AN: 4822

European-Finnish (FIN) AF: 0.182 AC: 1928 AN: 10590

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14040 AN: 67966

Other (OTH) AF: 0.277 AC: 587 AN: 2116

Alfa AF: 0.234 Hom.: 5694

Bravo AF: 0.288

Asia WGS AF: 0.274 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	21
DANN	Benign	0.56
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2658997; hg19: chr2-193071438;