rs10136818

Variant names:

• chr14-25587311-A-T
• rs10136818

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 0.0278 in 152,274 control chromosomes in the GnomAD database, including 117 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 0.028 (117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 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: 0.0277 AC: 4213 AN: 152156 Hom.: 117 Cov.: 32

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00795

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0278 AC: 4229 AN: 152274 Hom.: 117 Cov.: 32 AF XY: 0.0290 AC XY: 2160 AN XY: 74468

African (AFR) AF: 0.0498 AC: 2068 AN: 41564

American (AMR) AF: 0.0285 AC: 435 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3464

East Asian (EAS) AF: 0.129 AC: 667 AN: 5174

South Asian (SAS) AF: 0.0342 AC: 165 AN: 4824

European-Finnish (FIN) AF: 0.0163 AC: 173 AN: 10620

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00797 AC: 542 AN: 68024

Other (OTH) AF: 0.0260 AC: 55 AN: 2114

Alfa AF: 0.0195 Hom.: 8

Bravo AF: 0.0310

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.82
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10136818; hg19: chr14-26056517;