rs10497551

Variant names:

• chr2-179916817-C-T
• rs10497551

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 0.146 in 152,060 control chromosomes in the GnomAD database, including 2,041 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 0.15 (2041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 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: 0.146 AC: 22203 AN: 151942 Hom.: 2032 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.0872

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.146 AC: 22227 AN: 152060 Hom.: 2041 Cov.: 32 AF XY: 0.154 AC XY: 11448 AN XY: 74326

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.0872

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.128

Alfa AF: 0.141 Hom.: 215

Bravo AF: 0.152

Asia WGS AF: 0.197 AC: 683 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497551; hg19: chr2-180781544;