14-55987356-C-T

Variant names:

• chr14-55987356-C-T
• rs1188157

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.616 in 151,984 control chromosomes in the GnomAD database, including 30,092 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 0.62 (30092 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 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: 0.616 AC: 93495 AN: 151866 Hom.: 30048 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.616 AC: 93595 AN: 151984 Hom.: 30092 Cov.: 31 AF XY: 0.606 AC XY: 45048 AN XY: 74290

African (AFR) AF: 0.817 AC: 33896 AN: 41498

American (AMR) AF: 0.553 AC: 8446 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3466

East Asian (EAS) AF: 0.580 AC: 2984 AN: 5146

South Asian (SAS) AF: 0.421 AC: 2025 AN: 4814

European-Finnish (FIN) AF: 0.460 AC: 4850 AN: 10550

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.554 AC: 37640 AN: 67930

Other (OTH) AF: 0.617 AC: 1299 AN: 2106

Alfa AF: 0.566 Hom.: 38301

Bravo AF: 0.637

Asia WGS AF: 0.486 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.58
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1188157; hg19: chr14-56454074;