rs6525038

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000237311 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.817 AC: 24673 AN: 30189

American (AMR) AF: 0.199 AC: 2088 AN: 10487

Ashkenazi Jewish (ASJ) AF: 0.0982 AC: 260 AN: 2647

East Asian (EAS) AF: 0.000560 AC: 2 AN: 3569

South Asian (SAS) AF: 0.0806 AC: 213 AN: 2642

European-Finnish (FIN) AF: 0.0685 AC: 413 AN: 6029

Middle Eastern (MID) AF: 0.156 AC: 34 AN: 218

European-Non Finnish (NFE) AF: 0.0966 AC: 5120 AN: 52978

Other (OTH) AF: 0.237 AC: 361 AN: 1521

Alfa AF: 0.166 Hom.: 16366

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
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs6525038; hg19: chrX-65193018;