rs10518115

Variant names:

• chr4-73540998-A-T
• rs10518115

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 0.2 in 152,160 control chromosomes in the GnomAD database, including 3,780 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 (3780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 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: 0.200 AC: 30367 AN: 152046 Hom.: 3774 Cov.: 32

Gnomad AFR AF: 0.0545

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.200 AC: 30384 AN: 152160 Hom.: 3780 Cov.: 32 AF XY: 0.202 AC XY: 15053 AN XY: 74368

African (AFR) AF: 0.0545 AC: 2263 AN: 41540

American (AMR) AF: 0.355 AC: 5437 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3472

East Asian (EAS) AF: 0.233 AC: 1208 AN: 5180

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4816

European-Finnish (FIN) AF: 0.214 AC: 2263 AN: 10564

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16240 AN: 67978

Other (OTH) AF: 0.246 AC: 519 AN: 2106

Alfa AF: 0.215 Hom.: 466

Bravo AF: 0.202

Asia WGS AF: 0.262 AC: 910 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	7.4
DANN	Benign	0.57
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs10518115; hg19: chr4-74406715;