rs5904726

Positions:

• chrX-147241105-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000639829.1(ENSG00000284377):​n.411+12547A>G variant causes a intron, non coding transcript 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: ENST00000639829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105373347	XR_005647084.2	n.157+22811A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000639829.1	n.411+12547A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000701574.1	n.204+22811A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.429 AC: 47617 AN: 110963 Hom.: 7572 Cov.: 23 AF XY: 0.412 AC XY: 13670 AN XY: 33191

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

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.396

Alfa AF: 0.404 Hom.: 29886

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5904726; hg19: chrX-146322623;