rs6525038

Variant names:

• chrX-65973176-A-G
• rs6525038
• ENST00000650998.1:n.155-27246A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650998.1(ENSG00000237311):​n.155-27246A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 110,954 control chromosomes in the GnomAD database, including 7,866 homozygotes. There are 9,147 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 0.30 (7866 hom., 9147 hem., cov: 22)
• Consequence: ENSG00000237311 ENST00000650998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

Genes affected

ENSG00000237311 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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
ENSG00000237311	ENST00000650998.1	n.155-27246A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.300 AC: 33256 AN: 110901 Hom.: 7857 Cov.: 22 AF XY: 0.274 AC XY: 9090 AN XY: 33153

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.000559

Gnomad SAS AF: 0.0789

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0967

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.300 AC: 33328 AN: 110954 Hom.: 7866 Cov.: 22 AF XY: 0.275 AC XY: 9147 AN XY: 33216

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.0982

Gnomad4 EAS AF: 0.000560

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0966

Gnomad4 OTH AF: 0.237

Alfa AF: 0.136 Hom.: 8015

Bravo AF: 0.335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6525038; hg19: chrX-65193018;