rs2488073

Variant names:

• chr10-92739218-A-G
• rs2488073

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 0.412 in 151,816 control chromosomes in the GnomAD database, including 13,776 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 0.41 (13776 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62564 AN: 151698 Hom.: 13776 Cov.: 30

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.412 AC: 62585 AN: 151816 Hom.: 13776 Cov.: 30 AF XY: 0.413 AC XY: 30655 AN XY: 74204

African (AFR) AF: 0.280 AC: 11606 AN: 41394

American (AMR) AF: 0.469 AC: 7143 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1092 AN: 5158

South Asian (SAS) AF: 0.298 AC: 1432 AN: 4802

European-Finnish (FIN) AF: 0.528 AC: 5562 AN: 10532

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32877 AN: 67920

Other (OTH) AF: 0.413 AC: 873 AN: 2112

Alfa AF: 0.444 Hom.: 1966

Bravo AF: 0.401

Asia WGS AF: 0.290 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.3
DANN	Benign	0.57
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2488073; hg19: chr10-94498975;