rs2364115

chr10-22528790-C-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 0.731 in 152,078 control chromosomes in the GnomAD database, including 41,107 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 0.73 (41107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 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: 0.731 AC: 111044 AN: 151960 Hom.: 41061 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.731 AC: 111152 AN: 152078 Hom.: 41107 Cov.: 32 AF XY: 0.735 AC XY: 54625 AN XY: 74340

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.745

Alfa AF: 0.707 Hom.: 4745

Bravo AF: 0.739

Asia WGS AF: 0.732 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.44
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2364115; hg19: chr10-22817719;