rs10497452

chr2-176201788-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 168 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0465

Gnomad4 AMR AF: 0.0336

Gnomad4 ASJ AF: 0.0469

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.0363

Gnomad4 NFE AF: 0.0496

Gnomad4 OTH AF: 0.0458

Alfa AF: 0.0474 Hom.: 40

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497452; hg19: chr2-177066516;