rs2488075

Variant names:

• chr10-92730417-T-C
• rs2488075

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 0.394 in 151,036 control chromosomes in the GnomAD database, including 13,198 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 0.39 (13198 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.394 AC: 59457 AN: 150924 Hom.: 13200 Cov.: 27

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.394 AC: 59473 AN: 151036 Hom.: 13198 Cov.: 27 AF XY: 0.397 AC XY: 29261 AN XY: 73742

African (AFR) AF: 0.220 AC: 9071 AN: 41270

American (AMR) AF: 0.433 AC: 6575 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1329 AN: 3458

East Asian (EAS) AF: 0.135 AC: 697 AN: 5150

South Asian (SAS) AF: 0.326 AC: 1541 AN: 4722

European-Finnish (FIN) AF: 0.544 AC: 5648 AN: 10376

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.493 AC: 33336 AN: 67610

Other (OTH) AF: 0.416 AC: 865 AN: 2078

Alfa AF: 0.406 Hom.: 2013

Bravo AF: 0.378

Asia WGS AF: 0.274 AC: 944 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	14
DANN	Benign	0.78
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2488075; hg19: chr10-94490174; COSMIC: COSV69045543;