chrX-83504705-G-T

Variant names:

• chrX-83504705-G-T
• rs5922814
• ENST00000782953.1:n.287-1022C>A

Variant summary

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

The ENST00000782953.1(ENSG00000301928):​n.287-1022C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 110,478 control chromosomes in the GnomAD database, including 7,721 homozygotes. There are 13,437 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 0.42 (7721 hom., 13437 hem., cov: 22)
• Consequence: ENSG00000301928 ENST00000782953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 0 publications found

Genes affected

ENSG00000301928 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985635	XR_001755986.2	n.74-1022C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301928	ENST00000782953.1	n.287-1022C>A		intron_variant	Intron 2 of 3
ENSG00000301928	ENST00000782954.1	n.295-1022C>A		intron_variant	Intron 2 of 3
ENSG00000301928	ENST00000782955.1	n.436-1022C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.418 AC: 46142 AN: 110427 Hom.: 7729 Cov.: 22

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.502

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.417 AC: 46119 AN: 110478 Hom.: 7721 Cov.: 22 AF XY: 0.410 AC XY: 13437 AN XY: 32752

African (AFR) AF: 0.218 AC: 6624 AN: 30440

American (AMR) AF: 0.361 AC: 3787 AN: 10477

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1472 AN: 2629

East Asian (EAS) AF: 0.618 AC: 2110 AN: 3415

South Asian (SAS) AF: 0.281 AC: 742 AN: 2639

European-Finnish (FIN) AF: 0.558 AC: 3227 AN: 5780

Middle Eastern (MID) AF: 0.479 AC: 101 AN: 211

European-Non Finnish (NFE) AF: 0.513 AC: 27056 AN: 52703

Other (OTH) AF: 0.441 AC: 663 AN: 1502

Alfa AF: 0.434 Hom.: 3390

Bravo AF: 0.402

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs5922814; hg19: chrX-82759713;