rs11157994

Positions:

• chr14-53984584-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;