ENST00000659022.1:n.1043-51730T>C

Variant names:

• chrX-8317834-T-C
• rs4830576
• ENST00000659022.1:n.1043-51730T>C

Variant summary

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

The ENST00000659022.1(ENSG00000285679):​n.1043-51730T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 110,145 control chromosomes in the GnomAD database, including 4,716 homozygotes. There are 10,985 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 0.34 (4716 hom., 10985 hem., cov: 22)
• Consequence: ENSG00000285679 ENST00000659022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 4 publications found

Genes affected

ENSG00000285679 (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 (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985675	XR_001755782.2	n.1985+89429T>C		intron_variant	Intron 2 of 3
LOC107985675	XR_001755783.2	n.1985+89429T>C		intron_variant	Intron 2 of 4
LOC107985675	XR_001755784.2	n.1985+89429T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285679	ENST00000659022.1	n.1043-51730T>C		intron_variant	Intron 2 of 3
ENSG00000285679	ENST00000746116.1	n.71+89429T>C		intron_variant	Intron 1 of 4
ENSG00000285679	ENST00000746117.1	n.71+89429T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 37823 AN: 110090 Hom.: 4719 Cov.: 22

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.344 AC: 37838 AN: 110145 Hom.: 4716 Cov.: 22 AF XY: 0.339 AC XY: 10985 AN XY: 32439

African (AFR) AF: 0.264 AC: 8013 AN: 30363

American (AMR) AF: 0.413 AC: 4262 AN: 10312

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1053 AN: 2620

East Asian (EAS) AF: 0.482 AC: 1659 AN: 3441

South Asian (SAS) AF: 0.367 AC: 942 AN: 2568

European-Finnish (FIN) AF: 0.278 AC: 1606 AN: 5785

Middle Eastern (MID) AF: 0.469 AC: 100 AN: 213

European-Non Finnish (NFE) AF: 0.367 AC: 19358 AN: 52682

Other (OTH) AF: 0.355 AC: 531 AN: 1496

Alfa AF: 0.363 Hom.: 41160

Bravo AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.87
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs4830576; hg19: chrX-8285875;