rs10497452

Variant names:

• chr2-176201788-C-T
• rs10497452

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0438 in 152,024 control chromosomes in the GnomAD database, including 169 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 (169 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0438 (6654/152024) while in subpopulation NFE AF = 0.0496 (3368/67964). AF 95% confidence interval is 0.0482. There are 169 homozygotes in GnomAd4. There are 3149 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 169 gene

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: 0.0437 AC: 6642 AN: 151906 Hom.: 168 Cov.: 33

Gnomad AFR AF: 0.0462

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.0363

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.0463

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

GnomAD4 genome AF: 0.0438 AC: 6654 AN: 152024 Hom.: 169 Cov.: 33 AF XY: 0.0424 AC XY: 3149 AN XY: 74294

African (AFR) AF: 0.0465 AC: 1925 AN: 41432

American (AMR) AF: 0.0336 AC: 513 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.0354 AC: 171 AN: 4824

European-Finnish (FIN) AF: 0.0363 AC: 383 AN: 10554

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0496 AC: 3368 AN: 67964

Other (OTH) AF: 0.0458 AC: 97 AN: 2116

Alfa AF: 0.0474 Hom.: 41

Bravo AF: 0.0442

Asia WGS AF: 0.0190 AC: 67 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.82
DANN	Benign	0.62
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10497452; hg19: chr2-177066516;