rs10497435

Positions:

• chr2-175182940-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 0.0436 in 152,282 control chromosomes in the GnomAD database, including 183 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 0.044 (183 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.868

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 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: 0.0436 AC: 6629 AN: 152164 Hom.: 182 Cov.: 32

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0472

Gnomad OTH AF: 0.0527

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0436 AC: 6632 AN: 152282 Hom.: 183 Cov.: 32 AF XY: 0.0432 AC XY: 3214 AN XY: 74474

Gnomad4 AFR AF: 0.0265

Gnomad4 AMR AF: 0.0440

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.0645

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.0472

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0426 Hom.: 27

Bravo AF: 0.0443

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	9.6
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497435; hg19: chr2-176047668;