rs1953743

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.

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.265-331G>A		intron	N/A
	ENSG00000297427	ENST00000747858.1		n.366-331G>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs1953743;

hg19: chr14-54652479;