rs3116754

Variant names:

• chrX-129641598-T-A
• rs3116754
• ENST00000835926.1:n.241-1702T>A

Variant summary

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

The ENST00000835926.1(ENSG00000308713):​n.241-1702T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 110,474 control chromosomes in the GnomAD database, including 7,511 homozygotes. There are 9,442 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 0.30 (7511 hom., 9442 hem., cov: 22)
• Consequence: ENSG00000308713 ENST00000835926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 2 publications found

Genes affected

ENSG00000308713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835926.1. 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
	ENSG00000308713	ENST00000835926.1		n.241-1702T>A		intron	N/A
	ENSG00000308713	ENST00000835927.1		n.241-1119T>A		intron	N/A
	ENSG00000308713	ENST00000835928.1		n.241-1702T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 33474 AN: 110421 Hom.: 7504 Cov.: 22

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.303 AC: 33527 AN: 110474 Hom.: 7511 Cov.: 22 AF XY: 0.288 AC XY: 9442 AN XY: 32796

African (AFR) AF: 0.763 AC: 22921 AN: 30027

American (AMR) AF: 0.258 AC: 2692 AN: 10453

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 252 AN: 2636

East Asian (EAS) AF: 0.689 AC: 2363 AN: 3432

South Asian (SAS) AF: 0.238 AC: 624 AN: 2618

European-Finnish (FIN) AF: 0.0569 AC: 339 AN: 5961

Middle Eastern (MID) AF: 0.108 AC: 23 AN: 213

European-Non Finnish (NFE) AF: 0.0737 AC: 3900 AN: 52930

Other (OTH) AF: 0.272 AC: 413 AN: 1519

Alfa AF: 0.0153 Hom.: 54

Bravo AF: 0.350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs3116754; hg19: chrX-128775575;