rs972635

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000226530 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000226530	ENST00000455931.2	n.757+28155T>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 35899 AN: 109482 Hom.: 4714 Cov.: 22 AF XY: 0.311 AC XY: 9921 AN XY: 31918

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

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0595

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.306

Alfa AF: 0.332 Hom.: 2149

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs972635; hg19: chrX-51167688;