chrX-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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804502.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304551	ENST00000804502.1		n.72-30458C>A		intron	N/A

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 v4.9

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;