rs5929554

Variant names:

• chrX-113089796-T-A
• rs5929554
• ENST00000651919.1:n.346+16678T>A

Variant summary

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

The ENST00000651919.1(ENSG00000286072):​n.346+16678T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 110,002 control chromosomes in the GnomAD database, including 7,160 homozygotes. There are 13,176 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 0.41 (7160 hom., 13176 hem., cov: 22)
• Consequence: ENSG00000286072 ENST00000651919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 1 publications found

Genes affected

ENSG00000286072 (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 (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928437	NR_110399.2	n.115+16678T>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286072	ENST00000651919.1	n.346+16678T>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.412 AC: 45333 AN: 109951 Hom.: 7165 Cov.: 22

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.412 AC: 45334 AN: 110002 Hom.: 7160 Cov.: 22 AF XY: 0.408 AC XY: 13176 AN XY: 32328

African (AFR) AF: 0.256 AC: 7774 AN: 30330

American (AMR) AF: 0.403 AC: 4152 AN: 10311

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 1545 AN: 2627

East Asian (EAS) AF: 0.322 AC: 1113 AN: 3459

South Asian (SAS) AF: 0.520 AC: 1337 AN: 2571

European-Finnish (FIN) AF: 0.436 AC: 2524 AN: 5788

Middle Eastern (MID) AF: 0.427 AC: 91 AN: 213

European-Non Finnish (NFE) AF: 0.492 AC: 25849 AN: 52535

Other (OTH) AF: 0.415 AC: 623 AN: 1501

Alfa AF: 0.457 Hom.: 3223

Bravo AF: 0.401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs5929554; hg19: chrX-112333024;