rs10133840

Variant names:

• chr14-94944192-C-G
• rs10133840

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 0.788 in 152,112 control chromosomes in the GnomAD database, including 48,050 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 0.79 (48050 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.903 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: 0.788 AC: 119730 AN: 151994 Hom.: 47991 Cov.: 31

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.788 AC: 119847 AN: 152112 Hom.: 48050 Cov.: 31 AF XY: 0.788 AC XY: 58549 AN XY: 74346

African (AFR) AF: 0.911 AC: 37831 AN: 41532

American (AMR) AF: 0.865 AC: 13224 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2886 AN: 3470

East Asian (EAS) AF: 0.889 AC: 4587 AN: 5158

South Asian (SAS) AF: 0.832 AC: 4006 AN: 4814

European-Finnish (FIN) AF: 0.647 AC: 6836 AN: 10562

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47898 AN: 67982

Other (OTH) AF: 0.824 AC: 1736 AN: 2108

Alfa AF: 0.739 Hom.: 5276

Bravo AF: 0.812

Asia WGS AF: 0.838 AC: 2917 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	4.1
DANN	Benign	0.69
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10133840; hg19: chr14-95410529;