rs5904726

Variant names:

• chrX-147241105-A-G
• rs5904726
• ENST00000639829.1:n.411+12547A>G

Variant summary

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

The ENST00000639829.1(ENSG00000284377):​n.411+12547A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 111,017 control chromosomes in the GnomAD database, including 7,581 homozygotes. There are 13,698 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 0.43 (7581 hom., 13698 hem., cov: 23)
• Consequence: ENSG00000284377 ENST00000639829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 6 publications found

Genes affected

ENSG00000284377 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373347	XR_005647083.2	n.207+22811A>G		intron_variant	Intron 2 of 3
LOC105373347	XR_005647084.2	n.157+22811A>G		intron_variant	Intron 2 of 3
LOC105373347	XR_005647085.2	n.223+22811A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284377	ENST00000639829.1	n.411+12547A>G		intron_variant	Intron 3 of 4	5
ENSG00000284377	ENST00000701574.2	n.208+22811A>G		intron_variant	Intron 2 of 4
ENSG00000284377	ENST00000741835.1	n.308+12547A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.429 AC: 47617 AN: 110963 Hom.: 7572 Cov.: 23

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.429 AC: 47655 AN: 111017 Hom.: 7581 Cov.: 23 AF XY: 0.412 AC XY: 13698 AN XY: 33255

African (AFR) AF: 0.522 AC: 15900 AN: 30465

American (AMR) AF: 0.381 AC: 3973 AN: 10436

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1061 AN: 2633

East Asian (EAS) AF: 0.217 AC: 761 AN: 3509

South Asian (SAS) AF: 0.258 AC: 692 AN: 2678

European-Finnish (FIN) AF: 0.392 AC: 2323 AN: 5924

Middle Eastern (MID) AF: 0.239 AC: 51 AN: 213

European-Non Finnish (NFE) AF: 0.416 AC: 22009 AN: 52969

Other (OTH) AF: 0.396 AC: 598 AN: 1512

Alfa AF: 0.415 Hom.: 39066

Bravo AF: 0.436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.33
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs5904726; hg19: chrX-146322623;