14-54093300-T-C

Variant names:

• chr14-54093300-T-C
• rs1957636
• ENST00000747857.1:n.595-1203A>G

Variant summary

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

The ENST00000747857.1(ENSG00000297427):​n.595-1203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,874 control chromosomes in the GnomAD database, including 19,021 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 0.48 (19021 hom., cov: 31)
• Consequence: ENSG00000297427 ENST00000747857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 52 publications found

Genes affected

ENSG00000297427 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747857.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297427	ENST00000747857.1		n.595-1203A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72385 AN: 151756 Hom.: 19022 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.477 AC: 72393 AN: 151874 Hom.: 19021 Cov.: 31 AF XY: 0.475 AC XY: 35264 AN XY: 74226

African (AFR) AF: 0.243 AC: 10058 AN: 41434

American (AMR) AF: 0.507 AC: 7719 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2074 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1789 AN: 5150

South Asian (SAS) AF: 0.447 AC: 2149 AN: 4808

European-Finnish (FIN) AF: 0.574 AC: 6055 AN: 10556

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.601 AC: 40799 AN: 67912

Other (OTH) AF: 0.519 AC: 1096 AN: 2112

Alfa AF: 0.559 Hom.: 84954

Bravo AF: 0.462

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.0
DANN	Benign	0.74
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1957636;

hg19: chr14-54560018;