X-129643649-G-T

Variant names:

• chrX-129643649-G-T
• rs3131264
• ENST00000835929.1:n.590G>T

Variant summary

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

The ENST00000835929.1(ENSG00000308713):​n.590G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 110,839 control chromosomes in the GnomAD database, including 6,635 homozygotes. There are 8,260 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 0.26 (6635 hom., 8260 hem., cov: 22)
• Consequence: ENSG00000308713 ENST00000835929.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308713	ENST00000835929.1	n.590G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308713	ENST00000835930.1	n.1173G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308713	ENST00000835926.1	n.343+247G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 29154 AN: 110783 Hom.: 6626 Cov.: 22

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0780

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.113

Gnomad NFE AF: 0.0351

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.264 AC: 29214 AN: 110839 Hom.: 6635 Cov.: 22 AF XY: 0.250 AC XY: 8260 AN XY: 33077

African (AFR) AF: 0.737 AC: 22290 AN: 30247

American (AMR) AF: 0.208 AC: 2153 AN: 10371

Ashkenazi Jewish (ASJ) AF: 0.0780 AC: 206 AN: 2642

East Asian (EAS) AF: 0.510 AC: 1769 AN: 3469

South Asian (SAS) AF: 0.149 AC: 392 AN: 2635

European-Finnish (FIN) AF: 0.0285 AC: 171 AN: 6004

Middle Eastern (MID) AF: 0.100 AC: 22 AN: 219

European-Non Finnish (NFE) AF: 0.0350 AC: 1859 AN: 53042

Other (OTH) AF: 0.231 AC: 352 AN: 1523

Alfa AF: 0.224 Hom.: 2171

Bravo AF: 0.306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.56
DANN	Benign	0.29
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs3131264; hg19: chrX-128777626;