X-140156297-C-T

Variant names:

• chrX-140156297-C-T
• rs613278
• ENST00000758029.1:n.253-2621C>T

Variant summary

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

The ENST00000758029.1(ENSG00000298798):​n.253-2621C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 109,686 control chromosomes in the GnomAD database, including 8,852 homozygotes. There are 14,977 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 0.47 (8852 hom., 14977 hem., cov: 22)
• Consequence: ENSG00000298798 ENST00000758029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 0 publications found

Genes affected

ENSG00000298798 (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 = 0.521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758029.1. 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
	ENSG00000298798	ENST00000758029.1		n.253-2621C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.470 AC: 51529 AN: 109638 Hom.: 8845 Cov.: 22

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.470 AC: 51549 AN: 109686 Hom.: 8852 Cov.: 22 AF XY: 0.468 AC XY: 14977 AN XY: 32024

African (AFR) AF: 0.372 AC: 11242 AN: 30199

American (AMR) AF: 0.501 AC: 5179 AN: 10341

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1208 AN: 2624

East Asian (EAS) AF: 0.542 AC: 1825 AN: 3369

South Asian (SAS) AF: 0.433 AC: 1075 AN: 2482

European-Finnish (FIN) AF: 0.510 AC: 2965 AN: 5809

Middle Eastern (MID) AF: 0.373 AC: 78 AN: 209

European-Non Finnish (NFE) AF: 0.514 AC: 26964 AN: 52493

Other (OTH) AF: 0.473 AC: 711 AN: 1502

Alfa AF: 0.491 Hom.: 3946

Bravo AF: 0.466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs613278; hg19: chrX-139238459;