rs10497015

chr2-147620501-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 0.339 in 151,662 control chromosomes in the GnomAD database, including 9,020 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 0.34 (9020 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 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: 0.339 AC: 51433 AN: 151544 Hom.: 9024 Cov.: 30

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.339 AC: 51428 AN: 151662 Hom.: 9020 Cov.: 30 AF XY: 0.337 AC XY: 24950 AN XY: 74108

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.372

Alfa AF: 0.373 Hom.: 2633

Bravo AF: 0.334

Asia WGS AF: 0.249 AC: 865 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	9.3
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497015; hg19: chr2-148378069;