10-117997335-G-A

Variant names:

• chr10-117997335-G-A
• rs1986420

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 0.692 in 152,134 control chromosomes in the GnomAD database, including 43,219 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 0.69 (43219 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105221 AN: 152016 Hom.: 43226 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.692 AC: 105224 AN: 152134 Hom.: 43219 Cov.: 32 AF XY: 0.686 AC XY: 51006 AN XY: 74370

African (AFR) AF: 0.276 AC: 11451 AN: 41484

American (AMR) AF: 0.634 AC: 9686 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2924 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1167 AN: 5166

South Asian (SAS) AF: 0.807 AC: 3897 AN: 4828

European-Finnish (FIN) AF: 0.880 AC: 9326 AN: 10600

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.942 AC: 64082 AN: 67994

Other (OTH) AF: 0.747 AC: 1578 AN: 2112

Alfa AF: 0.613 Hom.: 4279

Bravo AF: 0.649

Asia WGS AF: 0.501 AC: 1746 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.18
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs1986420; hg19: chr10-119756846;