X-51424836-T-A

Variant names:

• chrX-51424836-T-A
• rs972635
• ENST00000455931.2:n.757+28155T>A

Variant summary

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

The ENST00000455931.2(ENSG00000226530):​n.757+28155T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 109,529 control chromosomes in the GnomAD database, including 4,720 homozygotes. There are 9,962 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 0.33 (4720 hom., 9962 hem., cov: 22)
• Consequence: ENSG00000226530 ENST00000455931.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 2 publications found

Genes affected

ENSG00000226530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455931.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226530	ENST00000455931.2	TSL:3	n.757+28155T>A		intron	N/A
	ENSG00000226530	ENST00000767703.1		n.736+28155T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 35899 AN: 109482 Hom.: 4714 Cov.: 22

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.328 AC: 35944 AN: 109529 Hom.: 4720 Cov.: 22 AF XY: 0.312 AC XY: 9962 AN XY: 31975

African (AFR) AF: 0.442 AC: 13345 AN: 30181

American (AMR) AF: 0.184 AC: 1892 AN: 10308

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 498 AN: 2623

East Asian (EAS) AF: 0.0595 AC: 209 AN: 3510

South Asian (SAS) AF: 0.246 AC: 626 AN: 2540

European-Finnish (FIN) AF: 0.354 AC: 2045 AN: 5777

Middle Eastern (MID) AF: 0.292 AC: 61 AN: 209

European-Non Finnish (NFE) AF: 0.318 AC: 16578 AN: 52198

Other (OTH) AF: 0.306 AC: 462 AN: 1512

Alfa AF: 0.332 Hom.: 2149

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.47
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs972635; hg19: chrX-51167688;