rs10497015

Variant names:

• chr2-147620501-T-C
• rs10497015

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 0.339 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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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 AC: 0.278877 AN: 0.278877

Gnomad4 AMR AF: 0.284 AC: 0.284212 AN: 0.284212

Gnomad4 ASJ AF: 0.455 AC: 0.454991 AN: 0.454991

Gnomad4 EAS AF: 0.231 AC: 0.230739 AN: 0.230739

Gnomad4 SAS AF: 0.295 AC: 0.295388 AN: 0.295388

Gnomad4 FIN AF: 0.347 AC: 0.346594 AN: 0.346594

Gnomad4 NFE AF: 0.390 AC: 0.390004 AN: 0.390004

Gnomad4 OTH AF: 0.372 AC: 0.372027 AN: 0.372027

Alfa AF: 0.365 Hom.: 4289

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;