rs6525038

chrX-65973176-A-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, non coding transcript 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: ENST00000650998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650998.1	n.155-27246A>G		intron_variant, non_coding_transcript_variant

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;