chrX-34073562-T-C

Variant names:

• chrX-34073562-T-C
• rs993010
• ENST00000653446.1:n.287-2904T>C

Variant summary

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

The ENST00000653446.1(ENSG00000233928):​n.287-2904T>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 0.56 (12865 hom., 17902 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000233928 ENST00000653446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 2 publications found

Genes affected

ENSG00000233928 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233928	ENST00000653446.1		n.287-2904T>C		intron	N/A
	ENSG00000233928	ENST00000656777.1		n.349-2904T>C		intron	N/A
	ENSG00000233928	ENST00000656973.1		n.201-2904T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 61633 AN: 110141 Hom.: 12871 Cov.: 22

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.645

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.571

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: 0.559 AC: 61631 AN: 110194 Hom.: 12865 Cov.: 22 AF XY: 0.550 AC XY: 17902 AN XY: 32532

African (AFR) AF: 0.425 AC: 12866 AN: 30298

American (AMR) AF: 0.502 AC: 5176 AN: 10307

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1497 AN: 2633

East Asian (EAS) AF: 0.270 AC: 937 AN: 3469

South Asian (SAS) AF: 0.416 AC: 1098 AN: 2638

European-Finnish (FIN) AF: 0.628 AC: 3660 AN: 5825

Middle Eastern (MID) AF: 0.653 AC: 139 AN: 213

European-Non Finnish (NFE) AF: 0.666 AC: 35061 AN: 52643

Other (OTH) AF: 0.570 AC: 852 AN: 1496

Alfa AF: 0.615 Hom.: 88290

Bravo AF: 0.542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.66
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs993010; hg19: chrX-34091679;