chrX-147591907-A-G

Variant names:

• chrX-147591907-A-G
• rs6626269
• ENST00000450437.1:n.3T>C

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000228855 ENST00000450437.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 0 publications found

Genes affected

ENSG00000228855 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228855	ENST00000450437.1	n.3T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.201 AC: 22201 AN: 110646 Hom.: 1700 Cov.: 22

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.217 AC: 6621 AN: 30522

American (AMR) AF: 0.153 AC: 1593 AN: 10405

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 341 AN: 2630

East Asian (EAS) AF: 0.233 AC: 813 AN: 3490

South Asian (SAS) AF: 0.191 AC: 501 AN: 2621

European-Finnish (FIN) AF: 0.185 AC: 1103 AN: 5977

Middle Eastern (MID) AF: 0.227 AC: 49 AN: 216

European-Non Finnish (NFE) AF: 0.205 AC: 10779 AN: 52671

Other (OTH) AF: 0.206 AC: 307 AN: 1493

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs6626269; hg19: chrX-146673425;