rs2488073

Positions:

• chr10-92739218-A-G

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 0.412 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.413

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2488073; hg19: chr10-94498975;