rs10133840

Variant names:

• chr14-94944192-C-G
• rs10133840

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.824

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10133840; hg19: chr14-95410529;