X-137340243-A-G

Variant names:

• chrX-137340243-A-G
• rs1413643
• ENST00000786458.1:n.167-11761A>G

Variant summary

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

The ENST00000786458.1(ENSG00000302412):​n.167-11761A>G 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 0.84 (29000 hom., 27705 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000302412 ENST00000786458.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.37
• Publications: 0 publications found

Genes affected

ENSG00000302412 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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
ENSG00000302412	ENST00000786458.1	n.167-11761A>G		intron_variant	Intron 2 of 5
ENSG00000302412	ENST00000786459.1	n.207-11761A>G		intron_variant	Intron 3 of 6
ENSG00000302412	ENST00000786460.1	n.232-11761A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.842 AC: 92931 AN: 110435 Hom.: 29019 Cov.: 22

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.941

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.868

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: 0.841 AC: 92951 AN: 110492 Hom.: 29000 Cov.: 22 AF XY: 0.846 AC XY: 27705 AN XY: 32734

African (AFR) AF: 0.523 AC: 15871 AN: 30353

American (AMR) AF: 0.894 AC: 9301 AN: 10403

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 2596 AN: 2637

East Asian (EAS) AF: 0.752 AC: 2573 AN: 3423

South Asian (SAS) AF: 0.938 AC: 2395 AN: 2552

European-Finnish (FIN) AF: 0.988 AC: 5783 AN: 5854

Middle Eastern (MID) AF: 0.940 AC: 203 AN: 216

European-Non Finnish (NFE) AF: 0.988 AC: 52244 AN: 52867

Other (OTH) AF: 0.867 AC: 1305 AN: 1506

Alfa AF: 0.920 Hom.: 40303

Bravo AF: 0.821

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.70
PhyloP100		-4.4

Splicing

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

Other links and lift over

dbSNP: rs1413643; hg19: chrX-136422402;