rs6626269

Positions:

• chrX-147591907-A-G

Variant summary

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

The ENST00000450437.1(ENSG00000228855):​n.3T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 110,699 control chromosomes in the GnomAD database, including 1,703 homozygotes. There are 6,367 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 0.20 (1703 hom., 6366 hem., cov: 22)
  • Exomes 𝑓: 0.50 (0 hom. 1 hem.)
• Consequence: ENST00000450437.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000450437.1	n.3T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 22201 AN: 110646 Hom.: 1700 Cov.: 22 AF XY: 0.193 AC XY: 6354 AN XY: 32972

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.204

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.201 AC: 22215 AN: 110697 Hom.: 1703 Cov.: 22 AF XY: 0.193 AC XY: 6366 AN XY: 33033

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.206

Alfa AF: 0.205 Hom.: 1269

Bravo AF: 0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6626269; hg19: chrX-146673425;