X-38140399-A-T

Variant names:

• chrX-38140399-A-T
• rs56156506
• ENST00000465127.1:c.172-525722A>T

Variant summary

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

The ENST00000465127.1(ENSG00000250349):​c.172-525722A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 111,476 control chromosomes in the GnomAD database, including 5,948 homozygotes. There are 10,384 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 0.32 (5948 hom., 10384 hem., cov: 23)
• Consequence: ENSG00000250349 ENST00000465127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465127.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250349	ENST00000465127.1	TSL:5	c.172-525722A>T		intron	N/A	ENSP00000417050.1	B4E171

Frequencies

GnomAD3 genomes AF: 0.322 AC: 35855 AN: 111418 Hom.: 5940 Cov.: 23

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.262

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.322 AC: 35890 AN: 111476 Hom.: 5948 Cov.: 23 AF XY: 0.308 AC XY: 10384 AN XY: 33712

African (AFR) AF: 0.634 AC: 19348 AN: 30515

American (AMR) AF: 0.338 AC: 3559 AN: 10526

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 491 AN: 2638

East Asian (EAS) AF: 0.120 AC: 424 AN: 3536

South Asian (SAS) AF: 0.343 AC: 915 AN: 2666

European-Finnish (FIN) AF: 0.102 AC: 625 AN: 6105

Middle Eastern (MID) AF: 0.268 AC: 56 AN: 209

European-Non Finnish (NFE) AF: 0.186 AC: 9893 AN: 53077

Other (OTH) AF: 0.318 AC: 484 AN: 1523

Alfa AF: 0.108 Hom.: 544

Bravo AF: 0.354

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.85
PhyloP100		-0.28

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs56156506;

hg19: chrX-37999652;