rs10187560

chr2-173060323-T-Cchr2-173060323-T-G

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 0.614 in 151,912 control chromosomes in the GnomAD database, including 29,371 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 0.61 (29371 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

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 (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

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: 0.614 AC: 93191 AN: 151792 Hom.: 29376 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.614 AC: 93213 AN: 151912 Hom.: 29371 Cov.: 31 AF XY: 0.605 AC XY: 44894 AN XY: 74232

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.582

Alfa AF: 0.658 Hom.: 16051

Bravo AF: 0.596

Asia WGS AF: 0.387 AC: 1350 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	2.5
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10187560; hg19: chr2-173925051;