rs11159647

Variant names:

• chr14-84308865-G-A
• rs11159647

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 0.337 in 151,940 control chromosomes in the GnomAD database, including 10,690 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 0.34 (10690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 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: 0.337 AC: 51208 AN: 151822 Hom.: 10690 Cov.: 32

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.337 AC: 51194 AN: 151940 Hom.: 10690 Cov.: 32 AF XY: 0.337 AC XY: 24999 AN XY: 74240

Gnomad4 AFR AF: 0.0913

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.376

Alfa AF: 0.422 Hom.: 7045

Bravo AF: 0.329

Asia WGS AF: 0.368 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11159647; hg19: chr14-84775209;