rs363371

Variant names:

• chr10-117226885-G-A
• rs363371

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 0.199 in 152,128 control chromosomes in the GnomAD database, including 3,658 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 0.20 (3658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30269 AN: 152010 Hom.: 3649 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.199 AC: 30298 AN: 152128 Hom.: 3658 Cov.: 32 AF XY: 0.199 AC XY: 14823 AN XY: 74364

African (AFR) AF: 0.119 AC: 4932 AN: 41502

American (AMR) AF: 0.155 AC: 2366 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3464

East Asian (EAS) AF: 0.558 AC: 2878 AN: 5160

South Asian (SAS) AF: 0.330 AC: 1593 AN: 4820

European-Finnish (FIN) AF: 0.174 AC: 1844 AN: 10580

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15307 AN: 67986

Other (OTH) AF: 0.192 AC: 406 AN: 2116

Alfa AF: 0.204 Hom.: 4889

Bravo AF: 0.194

Asia WGS AF: 0.437 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.96
DANN	Benign	0.63
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs363371; hg19: chr10-118986396;