X-86937000-G-T

Variant names:

• chrX-86937000-G-T
• rs2710057
• ENST00000804502.1:n.72-30458C>A

Variant summary

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

The ENST00000804502.1(ENSG00000304551):​n.72-30458C>A 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 0.72 (20504 hom., 23064 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000304551 ENST00000804502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 6 publications found

Genes affected

ENSG00000304551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).

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
ENSG00000304551	ENST00000804502.1	n.72-30458C>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.721 AC: 79308 AN: 109926 Hom.: 20506 Cov.: 22

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.734

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: InbreedingCoeff AF: 0.722 AC: 79359 AN: 109980 Hom.: 20504 Cov.: 22 AF XY: 0.715 AC XY: 23064 AN XY: 32254

African (AFR) AF: 0.736 AC: 22248 AN: 30226

American (AMR) AF: 0.841 AC: 8649 AN: 10288

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 1821 AN: 2631

East Asian (EAS) AF: 0.837 AC: 2875 AN: 3436

South Asian (SAS) AF: 0.524 AC: 1358 AN: 2594

European-Finnish (FIN) AF: 0.636 AC: 3644 AN: 5726

Middle Eastern (MID) AF: 0.676 AC: 142 AN: 210

European-Non Finnish (NFE) AF: 0.705 AC: 37151 AN: 52704

Other (OTH) AF: 0.732 AC: 1096 AN: 1497

Alfa AF: 0.713 Hom.: 107505

Bravo AF: 0.743

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.61
DANN	Benign	0.47
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2710057; hg19: chrX-86192003;