rs5990560

Variant names:

• chrX-96406563-A-T
• rs5990560
• ENST00000729575.1:n.149-11689T>A

Variant summary

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

The ENST00000729575.1(ENSG00000295365):​n.149-11689T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 109,554 control chromosomes in the GnomAD database, including 6,759 homozygotes. There are 10,703 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 0.35 (6759 hom., 10703 hem., cov: 22)
• Consequence: ENSG00000295365 ENST00000729575.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01
• Publications: 1 publications found

Genes affected

ENSG00000295365 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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
ENSG00000295365	ENST00000729575.1	n.149-11689T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.346 AC: 37883 AN: 109505 Hom.: 6752 Cov.: 22

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.346 AC: 37935 AN: 109554 Hom.: 6759 Cov.: 22 AF XY: 0.334 AC XY: 10703 AN XY: 31998

African (AFR) AF: 0.694 AC: 20697 AN: 29820

American (AMR) AF: 0.244 AC: 2527 AN: 10340

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 695 AN: 2615

East Asian (EAS) AF: 0.511 AC: 1745 AN: 3413

South Asian (SAS) AF: 0.425 AC: 1061 AN: 2496

European-Finnish (FIN) AF: 0.189 AC: 1115 AN: 5889

Middle Eastern (MID) AF: 0.295 AC: 62 AN: 210

European-Non Finnish (NFE) AF: 0.178 AC: 9359 AN: 52607

Other (OTH) AF: 0.334 AC: 499 AN: 1492

Alfa AF: 0.270 Hom.: 1768

Bravo AF: 0.367

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.60
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs5990560; hg19: chrX-95661562;