rs5945326

Variant names:

• chrX-153634467-A-G
• rs5945326
• ENST00000746876.1:n.227T>C

Variant summary

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

The ENST00000746876.1(ENSG00000297294):​n.227T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 110,701 control chromosomes in the GnomAD database, including 2,809 homozygotes. There are 8,363 hemizygotes in GnomAD. 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 0.25 (2809 hom., 8363 hem., cov: 22)
• Consequence: ENSG00000297294 ENST00000746876.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 99 publications found

Genes affected

ENSG00000297294 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.425 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
ENSG00000297294	ENST00000746876.1	n.227T>C		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000297294	ENST00000746877.1	n.216T>C		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000297294	ENST00000746878.1	n.304T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 28019 AN: 110648 Hom.: 2801 Cov.: 22

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.253 AC: 28033 AN: 110701 Hom.: 2809 Cov.: 22 AF XY: 0.254 AC XY: 8363 AN XY: 32981

African (AFR) AF: 0.203 AC: 6205 AN: 30495

American (AMR) AF: 0.436 AC: 4549 AN: 10436

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 468 AN: 2640

East Asian (EAS) AF: 0.375 AC: 1302 AN: 3470

South Asian (SAS) AF: 0.380 AC: 980 AN: 2579

European-Finnish (FIN) AF: 0.271 AC: 1603 AN: 5921

Middle Eastern (MID) AF: 0.171 AC: 37 AN: 216

European-Non Finnish (NFE) AF: 0.234 AC: 12358 AN: 52764

Other (OTH) AF: 0.260 AC: 392 AN: 1510

Alfa AF: 0.245 Hom.: 24345

Bravo AF: 0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.69
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs5945326; hg19: chrX-152899922;