rs2295814

chr10-62811516-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0556 in 152,304 control chromosomes in the GnomAD database, including 311 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 0.056 (311 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 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: 0.0556 AC: 8461 AN: 152186 Hom.: 309 Cov.: 33

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0556 AC: 8471 AN: 152304 Hom.: 311 Cov.: 33 AF XY: 0.0557 AC XY: 4147 AN XY: 74476

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.0418

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0630

Gnomad4 FIN AF: 0.0627

Gnomad4 NFE AF: 0.0699

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0559 Hom.: 51

Bravo AF: 0.0535

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
Cadd	Benign	23
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2295814; hg19: chr10-64571276;