14-88561547-G-C

Variant names:

• chr14-88561547-G-C
• rs11159859

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 0.569 in 151,942 control chromosomes in the GnomAD database, including 26,878 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 0.57 (26878 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.688 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: 0.570 AC: 86486 AN: 151824 Hom.: 26884 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.569 AC: 86503 AN: 151942 Hom.: 26878 Cov.: 31 AF XY: 0.575 AC XY: 42696 AN XY: 74272

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.622

Alfa AF: 0.499 Hom.: 1612

Bravo AF: 0.562

Asia WGS AF: 0.519 AC: 1807 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	1.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11159859; hg19: chr14-89027891;