chr10-117231271-G-A

Variant names:

• chr10-117231271-G-A
• rs363327

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 0.189 in 152,248 control chromosomes in the GnomAD database, including 4,884 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 0.19 (4884 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.955
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28740 AN: 152130 Hom.: 4860 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.0700

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.189 AC: 28807 AN: 152248 Hom.: 4884 Cov.: 33 AF XY: 0.186 AC XY: 13875 AN XY: 74432

African (AFR) AF: 0.446 AC: 18532 AN: 41516

American (AMR) AF: 0.208 AC: 3188 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0855 AC: 297 AN: 3472

East Asian (EAS) AF: 0.224 AC: 1159 AN: 5174

South Asian (SAS) AF: 0.0703 AC: 339 AN: 4822

European-Finnish (FIN) AF: 0.0458 AC: 486 AN: 10608

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4363 AN: 68030

Other (OTH) AF: 0.179 AC: 379 AN: 2116

Alfa AF: 0.0963 Hom.: 1467

Bravo AF: 0.220

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.74
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs363327; hg19: chr10-118990782;