rs10204426

chr2-85676785-C-Achr2-85676785-C-Gchr2-85676785-C-T

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 0.625 in 151,996 control chromosomes in the GnomAD database, including 30,066 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 0.62 (30066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 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: 0.624 AC: 94844 AN: 151878 Hom.: 30035 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.625 AC: 94925 AN: 151996 Hom.: 30066 Cov.: 32 AF XY: 0.623 AC XY: 46292 AN XY: 74276

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.626

Alfa AF: 0.608 Hom.: 19247

Bravo AF: 0.635

Asia WGS AF: 0.654 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.17
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10204426; hg19: chr2-85903908;