rs10497180

Variant names:

• chr2-157350754-C-T
• rs10497180

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 0.0302 in 152,292 control chromosomes in the GnomAD database, including 147 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 0.030 (147 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0851 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: 0.0301 AC: 4579 AN: 152174 Hom.: 146 Cov.: 33

Gnomad AFR AF: 0.0462

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.0617

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00757

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0302 AC: 4600 AN: 152292 Hom.: 147 Cov.: 33 AF XY: 0.0324 AC XY: 2412 AN XY: 74472

African (AFR) AF: 0.0467 AC: 1939 AN: 41556

American (AMR) AF: 0.0890 AC: 1361 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00605 AC: 21 AN: 3470

East Asian (EAS) AF: 0.0618 AC: 320 AN: 5178

South Asian (SAS) AF: 0.0406 AC: 196 AN: 4830

European-Finnish (FIN) AF: 0.0107 AC: 113 AN: 10608

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00757 AC: 515 AN: 68036

Other (OTH) AF: 0.0265 AC: 56 AN: 2116

Alfa AF: 0.0174 Hom.: 11

Bravo AF: 0.0366

Asia WGS AF: 0.0560 AC: 195 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10497180; hg19: chr2-158207266;