chrX-113174337-G-T

Variant names:

• chrX-113174337-G-T
• rs5974392
• ENST00000651919.1:n.347-37088G>T

Variant summary

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

The ENST00000651919.1(ENSG00000286072):​n.347-37088G>T 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 0.73 (21680 hom., 23822 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000286072 ENST00000651919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 1 publications found

Genes affected

ENSG00000286072 (HGNC:):

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651919.1. 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
	LOC101928437	NR_110399.2		n.231+62272G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286072	ENST00000651919.1		n.347-37088G>T		intron	N/A
	ENSG00000286767	ENST00000663700.2		n.74-12986G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.732 AC: 81050 AN: 110715 Hom.: 21680 Cov.: 23

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.746

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.725

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: 0.732 AC: 81104 AN: 110769 Hom.: 21680 Cov.: 23 AF XY: 0.722 AC XY: 23822 AN XY: 33001

African (AFR) AF: 0.907 AC: 27749 AN: 30600

American (AMR) AF: 0.692 AC: 7172 AN: 10368

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 1612 AN: 2635

East Asian (EAS) AF: 0.741 AC: 2602 AN: 3512

South Asian (SAS) AF: 0.641 AC: 1704 AN: 2659

European-Finnish (FIN) AF: 0.625 AC: 3634 AN: 5813

Middle Eastern (MID) AF: 0.749 AC: 161 AN: 215

European-Non Finnish (NFE) AF: 0.663 AC: 34984 AN: 52786

Other (OTH) AF: 0.727 AC: 1098 AN: 1510

Alfa AF: 0.704 Hom.: 5833

Bravo AF: 0.744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.16
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs5974392; hg19: chrX-112417564;