X-136973136-T-C

Variant names:

• chrX-136973136-T-C
• rs1190739

Variant summary

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

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 0.89 (31431 hom., 29836 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: TM9SF5P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 7 publications found

Genes affected

TM9SF5P (HGNC:55623): (transmembrane 9 superfamily member 5, pseudogene)

ENSG00000291054 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424306.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291054	ENST00000424306.5	TSL:2	n.2053-20350T>C		intron	N/A
	TM9SF5P	ENST00000426943.4	TSL:6	n.463+9685T>C		intron	N/A
	ENSG00000291054	ENST00000431464.7	TSL:2	n.526+47757T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.894 AC: 99283 AN: 111058 Hom.: 31438 Cov.: 23

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.916

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.911

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: 0.894 AC: 99311 AN: 111111 Hom.: 31431 Cov.: 23 AF XY: 0.896 AC XY: 29836 AN XY: 33295

African (AFR) AF: 0.738 AC: 22566 AN: 30579

American (AMR) AF: 0.919 AC: 9587 AN: 10430

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 2533 AN: 2649

East Asian (EAS) AF: 0.919 AC: 3234 AN: 3519

South Asian (SAS) AF: 0.987 AC: 2550 AN: 2584

European-Finnish (FIN) AF: 0.941 AC: 5499 AN: 5846

Middle Eastern (MID) AF: 0.908 AC: 197 AN: 217

European-Non Finnish (NFE) AF: 0.962 AC: 51076 AN: 53083

Other (OTH) AF: 0.912 AC: 1385 AN: 1519

Alfa AF: 0.930 Hom.: 99823

Bravo AF: 0.882

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.34
DANN	Benign	0.35
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1190739; hg19: chrX-136055295;