chr14-54919316-C-T

Variant names:

• chr14-54919316-C-T
• rs17128077

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 0.217 in 152,166 control chromosomes in the GnomAD database, including 5,027 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 0.22 (5027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 10 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 = 0.426 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: 0.217 AC: 32952 AN: 152048 Hom.: 5001 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0293

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.217 AC: 33021 AN: 152166 Hom.: 5027 Cov.: 32 AF XY: 0.214 AC XY: 15949 AN XY: 74398

African (AFR) AF: 0.431 AC: 17877 AN: 41476

American (AMR) AF: 0.118 AC: 1808 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 453 AN: 3472

East Asian (EAS) AF: 0.0293 AC: 152 AN: 5180

South Asian (SAS) AF: 0.201 AC: 970 AN: 4830

European-Finnish (FIN) AF: 0.152 AC: 1607 AN: 10590

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9612 AN: 68006

Other (OTH) AF: 0.160 AC: 338 AN: 2112

Alfa AF: 0.163 Hom.: 3829

Bravo AF: 0.222

Asia WGS AF: 0.157 AC: 547 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	0.29
DANN	Benign	0.51
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs17128077; hg19: chr14-55386034;