rs2488075

chr10-92730417-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.416

Alfa AF: 0.413 Hom.: 1998

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

Splicing

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

Publications

LitVar

Other links and lift over

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