chr14-54918609-C-G

Variant names:

• chr14-54918609-C-G
• rs943912

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 0.18 in 152,056 control chromosomes in the GnomAD database, including 2,544 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 0.18 (2544 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.218 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: 0.180 AC: 27318 AN: 151936 Hom.: 2543 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.180 AC: 27339 AN: 152056 Hom.: 2544 Cov.: 31 AF XY: 0.181 AC XY: 13487 AN XY: 74324

African (AFR) AF: 0.155 AC: 6443 AN: 41480

American (AMR) AF: 0.224 AC: 3419 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 460 AN: 3468

East Asian (EAS) AF: 0.139 AC: 721 AN: 5172

South Asian (SAS) AF: 0.122 AC: 590 AN: 4826

European-Finnish (FIN) AF: 0.241 AC: 2548 AN: 10556

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12457 AN: 67972

Other (OTH) AF: 0.188 AC: 396 AN: 2108

Alfa AF: 0.178 Hom.: 348

Bravo AF: 0.178

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.062
DANN	Benign	0.55
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs943912; hg19: chr14-55385327;