rs11157994

Variant names:

• chr14-53984584-A-G
• rs11157994

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 0.79 in 152,064 control chromosomes in the GnomAD database, including 50,161 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 (50161 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 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: 0.791 AC: 120151 AN: 151946 Hom.: 50150 Cov.: 31

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.790 AC: 120199 AN: 152064 Hom.: 50161 Cov.: 31 AF XY: 0.792 AC XY: 58904 AN XY: 74338

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.795

Alfa AF: 0.905 Hom.: 124709

Bravo AF: 0.757

Asia WGS AF: 0.756 AC: 2629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.14
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11157994; hg19: chr14-54451302;