rs2393886

chr10-62498584-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 0.57 in 152,004 control chromosomes in the GnomAD database, including 26,052 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 0.57 (26052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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: 0.570 AC: 86596 AN: 151884 Hom.: 25999 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.570 AC: 86708 AN: 152004 Hom.: 26052 Cov.: 32 AF XY: 0.568 AC XY: 42199 AN XY: 74298

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.536

Alfa AF: 0.516 Hom.: 5698

Bravo AF: 0.578

Asia WGS AF: 0.541 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	0.73
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2393886; hg19: chr10-64258343;