X-71186069-T-G

Variant names:

• chrX-71186069-T-G
• rs6624538
• ENST00000450860.1:n.268-2052A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000450860.1(ENSG00000228427):​n.268-2052A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., 0 hem., cov: 17)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 1 publications found

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.286-2052A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228427	ENST00000450860.1	n.268-2052A>C		intron_variant	Intron 1 of 1	3
ENSG00000228427	ENST00000652147.3	n.358-2056A>C		intron_variant	Intron 1 of 1
ENSG00000228427	ENST00000664514.4	n.600-2052A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 99991 Hom.: 0 Cov.: 17

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 100017 Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0 AN XY: 23855

African (AFR) AF: 0.00 AC: 0 AN: 27267

American (AMR) AF: 0.00 AC: 0 AN: 9003

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2498

East Asian (EAS) AF: 0.00 AC: 0 AN: 3087

South Asian (SAS) AF: 0.00 AC: 0 AN: 2038

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4402

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 193

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 49562

Other (OTH) AF: 0.00 AC: 0 AN: 1341

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.21
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6624538; hg19: chrX-70405919;