rs10497566

Positions:

• chr2-180516177-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 0.115 in 151,966 control chromosomes in the GnomAD database, including 1,477 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 0.12 (1477 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.934

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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: 0.115 AC: 17531 AN: 151848 Hom.: 1478 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0617

Gnomad ASJ AF: 0.0534

Gnomad EAS AF: 0.000582

Gnomad SAS AF: 0.0555

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.115 AC: 17541 AN: 151966 Hom.: 1477 Cov.: 32 AF XY: 0.111 AC XY: 8270 AN XY: 74294

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.0615

Gnomad4 ASJ AF: 0.0534

Gnomad4 EAS AF: 0.000584

Gnomad4 SAS AF: 0.0560

Gnomad4 FIN AF: 0.0606

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.100

Alfa AF: 0.103 Hom.: 152

Bravo AF: 0.121

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497566; hg19: chr2-181380904;