rs5934349

chrX-8042359-A-G

Variant summary

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

The ENST00000659022.1(ENSG00000285679):n.971+112946A>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 0.246 in 111,316 control chromosomes in the GnomAD database, including 2,666 homozygotes. There are 7,604 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 0.25 (2666 hom., 7604 hem., cov: 23)
• Consequence: ENST00000659022.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985675	XR_001755783.2	n.1914+112946A>G		intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755782.2	n.1914+112946A>G		intron_variant, non_coding_transcript_variant
LOC107985675	XR_001755784.2	n.1914+112946A>G		intron_variant, non_coding_transcript_variant
LOC107985675	XR_007068387.1	n.1914+112946A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659022.1	n.971+112946A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.246 AC: 27323 AN: 111268 Hom.: 2667 Cov.: 23 AF XY: 0.226 AC XY: 7573 AN XY: 33542

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0720

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.270

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.246 AC: 27355 AN: 111316 Hom.: 2666 Cov.: 23 AF XY: 0.226 AC XY: 7604 AN XY: 33600

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0719

Gnomad4 SAS AF: 0.0849

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.238

Alfa AF: 0.254 Hom.: 2039

Bravo AF: 0.249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.44
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5934349; hg19: chrX-8010400;