rs5954596

Variant names:

• chrX-142272785-C-T
• rs5954596
• ENST00000664519.1:n.368+48686C>T

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.368+48686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 111,072 control chromosomes in the GnomAD database, including 981 homozygotes. There are 4,675 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 0.15 (981 hom., 4675 hem., cov: 22)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 3 publications found

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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
ENSG00000288098	ENST00000664519.1	n.368+48686C>T		intron_variant	Intron 3 of 9

Frequencies

GnomAD3 genomes AF: 0.149 AC: 16528 AN: 111014 Hom.: 982 Cov.: 22

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0280

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.149 AC: 16530 AN: 111072 Hom.: 981 Cov.: 22 AF XY: 0.140 AC XY: 4675 AN XY: 33298

African (AFR) AF: 0.187 AC: 5716 AN: 30531

American (AMR) AF: 0.116 AC: 1209 AN: 10451

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 198 AN: 2633

East Asian (EAS) AF: 0.0278 AC: 98 AN: 3530

South Asian (SAS) AF: 0.175 AC: 452 AN: 2587

European-Finnish (FIN) AF: 0.129 AC: 772 AN: 5973

Middle Eastern (MID) AF: 0.164 AC: 35 AN: 214

European-Non Finnish (NFE) AF: 0.144 AC: 7608 AN: 52987

Other (OTH) AF: 0.125 AC: 186 AN: 1493

Alfa AF: 0.152 Hom.: 2087

Bravo AF: 0.151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.70
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs5954596; hg19: chrX-141360571;