X-38257469-T-C

Variant names:

• chrX-38257469-T-C
• rs10521410
• ENST00000465127.1:c.172-408652T>C

Variant summary

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

The ENST00000465127.1(ENSG00000250349):​c.172-408652T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0858 in 112,155 control chromosomes in the GnomAD database, including 461 homozygotes. There are 3,005 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 0.086 (461 hom., 3005 hem., cov: 22)
• Consequence: ENSG00000250349 ENST00000465127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 0 publications found

Genes affected

ENSG00000250349 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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
ENSG00000250349	ENST00000465127.1	c.172-408652T>C		intron_variant	Intron 3 of 8	5		ENSP00000417050.1

Frequencies

GnomAD3 genomes AF: 0.0856 AC: 9596 AN: 112104 Hom.: 458 Cov.: 22

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0251

Gnomad NFE AF: 0.0295

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0858 AC: 9624 AN: 112155 Hom.: 461 Cov.: 22 AF XY: 0.0875 AC XY: 3005 AN XY: 34343

African (AFR) AF: 0.162 AC: 4989 AN: 30844

American (AMR) AF: 0.116 AC: 1228 AN: 10581

Ashkenazi Jewish (ASJ) AF: 0.0181 AC: 48 AN: 2649

East Asian (EAS) AF: 0.188 AC: 667 AN: 3556

South Asian (SAS) AF: 0.182 AC: 491 AN: 2692

European-Finnish (FIN) AF: 0.0844 AC: 516 AN: 6116

Middle Eastern (MID) AF: 0.0229 AC: 5 AN: 218

European-Non Finnish (NFE) AF: 0.0295 AC: 1570 AN: 53286

Other (OTH) AF: 0.0719 AC: 110 AN: 1529

Alfa AF: 0.0570 Hom.: 5377

Bravo AF: 0.0947

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.81
PhyloP100		-0.27

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10521410; hg19: chrX-38116722;