ENST00000782953.1:n.358-863C>T

Variant names:

• chrX-83492771-G-A
• rs5968183
• ENST00000782953.1:n.358-863C>T

Variant summary

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

The ENST00000782953.1(ENSG00000301928):​n.358-863C>T 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 110,608 control chromosomes in the GnomAD database, including 7,652 homozygotes. There are 13,603 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 (7652 hom., 13603 hem., cov: 23)
• Consequence: ENSG00000301928 ENST00000782953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782953.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301928	ENST00000782953.1		n.358-863C>T		intron	N/A
	ENSG00000301928	ENST00000782954.1		n.366-863C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 46172 AN: 110556 Hom.: 7661 Cov.: 23

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.507

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.417 AC: 46148 AN: 110608 Hom.: 7652 Cov.: 23 AF XY: 0.413 AC XY: 13603 AN XY: 32924

African (AFR) AF: 0.217 AC: 6640 AN: 30650

American (AMR) AF: 0.363 AC: 3786 AN: 10425

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1476 AN: 2634

East Asian (EAS) AF: 0.617 AC: 2122 AN: 3442

South Asian (SAS) AF: 0.299 AC: 785 AN: 2624

European-Finnish (FIN) AF: 0.566 AC: 3301 AN: 5831

Middle Eastern (MID) AF: 0.482 AC: 96 AN: 199

European-Non Finnish (NFE) AF: 0.512 AC: 26949 AN: 52622

Other (OTH) AF: 0.438 AC: 659 AN: 1505

Alfa AF: 0.456 Hom.: 16633

Bravo AF: 0.400

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.40
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs5968183; hg19: chrX-82747779;