14-54185761-C-T

Variant names:

• chr14-54185761-C-T
• rs1953743
• ENST00000747857.1:n.265-331G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000747857.1(ENSG00000297427):​n.265-331G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,004 control chromosomes in the GnomAD database, including 19,651 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 (19651 hom., cov: 32)
• Consequence: ENSG00000297427 ENST00000747857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.856
• Publications: 9 publications found

Genes affected

ENSG00000297427 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370507	XR_001750980.2	n.335-331G>A		intron_variant	Intron 2 of 3
LOC105370507	XR_943882.3	n.335-331G>A		intron_variant	Intron 2 of 6
LOC105370507	XR_943883.3	n.335-331G>A		intron_variant	Intron 2 of 5
LOC105370507	XR_943884.2	n.335-331G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297427	ENST00000747857.1	n.265-331G>A		intron_variant	Intron 3 of 7
ENSG00000297427	ENST00000747858.1	n.366-331G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73197 AN: 151886 Hom.: 19652 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.482 AC: 73202 AN: 152004 Hom.: 19651 Cov.: 32 AF XY: 0.477 AC XY: 35459 AN XY: 74286

African (AFR) AF: 0.251 AC: 10409 AN: 41452

American (AMR) AF: 0.467 AC: 7132 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2148 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1404 AN: 5164

South Asian (SAS) AF: 0.391 AC: 1886 AN: 4818

European-Finnish (FIN) AF: 0.579 AC: 6104 AN: 10540

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42270 AN: 67968

Other (OTH) AF: 0.516 AC: 1089 AN: 2110

Alfa AF: 0.540 Hom.: 29818

Bravo AF: 0.463

Asia WGS AF: 0.385 AC: 1339 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	21
DANN	Benign	0.61
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs1953743; hg19: chr14-54652479;