rs2364115

Variant names:

• chr10-22528790-C-G
• rs2364115

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.843 AC: 34971 AN: 41480

American (AMR) AF: 0.799 AC: 12210 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3468

East Asian (EAS) AF: 0.662 AC: 3423 AN: 5172

South Asian (SAS) AF: 0.805 AC: 3883 AN: 4826

European-Finnish (FIN) AF: 0.672 AC: 7094 AN: 10558

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45169 AN: 67968

Other (OTH) AF: 0.745 AC: 1574 AN: 2114

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2364115; hg19: chr10-22817719;