rs10509714

Variant names:

• chr10-97798981-G-A
• rs10509714

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 0.104 in 151,902 control chromosomes in the GnomAD database, including 1,279 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 0.10 (1279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 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: 0.104 AC: 15808 AN: 151784 Hom.: 1282 Cov.: 32

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0882

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

GnomAD4 genome AF: 0.104 AC: 15804 AN: 151902 Hom.: 1279 Cov.: 32 AF XY: 0.115 AC XY: 8534 AN XY: 74224

African (AFR) AF: 0.0206 AC: 852 AN: 41454

American (AMR) AF: 0.0728 AC: 1112 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1545 AN: 5170

South Asian (SAS) AF: 0.254 AC: 1219 AN: 4806

European-Finnish (FIN) AF: 0.246 AC: 2580 AN: 10484

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.115 AC: 7781 AN: 67938

Other (OTH) AF: 0.0873 AC: 184 AN: 2108

Alfa AF: 0.111 Hom.: 1601

Bravo AF: 0.0859

Asia WGS AF: 0.235 AC: 815 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.70
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10509714; hg19: chr10-99558738;