X-137977928-C-T

Variant names:

• chrX-137977928-C-T
• rs2366516
• ENST00000636095.1:n.362-2362C>T

Variant summary

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

The ENST00000668975.1(ENSG00000283692):​n.262-2362C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 111,059 control chromosomes in the GnomAD database, including 386 homozygotes. There are 2,031 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 0.064 (386 hom., 2031 hem., cov: 22)
• Consequence: ENSG00000283692 ENST00000668975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 2 publications found

Genes affected

ENSG00000283692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668975.1. 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
	ENSG00000283692	ENST00000636095.1	TSL:5	n.362-2362C>T		intron	N/A
	ENSG00000283692	ENST00000637564.1	TSL:5	n.592-2362C>T		intron	N/A
	ENSG00000283692	ENST00000637685.1	TSL:5	n.315-2362C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 7050 AN: 111007 Hom.: 386 Cov.: 22

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.0413

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0254

Gnomad NFE AF: 0.0115

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0635 AC: 7056 AN: 111059 Hom.: 386 Cov.: 22 AF XY: 0.0609 AC XY: 2031 AN XY: 33343

African (AFR) AF: 0.130 AC: 3973 AN: 30569

American (AMR) AF: 0.0799 AC: 831 AN: 10403

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 185 AN: 2642

East Asian (EAS) AF: 0.338 AC: 1164 AN: 3441

South Asian (SAS) AF: 0.0422 AC: 111 AN: 2633

European-Finnish (FIN) AF: 0.0135 AC: 81 AN: 6016

Middle Eastern (MID) AF: 0.0279 AC: 6 AN: 215

European-Non Finnish (NFE) AF: 0.0115 AC: 609 AN: 52941

Other (OTH) AF: 0.0633 AC: 96 AN: 1516

Alfa AF: 0.0611 Hom.: 979

Bravo AF: 0.0761

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.69
PhyloP100		-0.24

Splicing

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: rs2366516;

hg19: chrX-137060087;