ENST00000837916.1:n.1190-31235A>G

Variant names:

• chrX-84770950-A-G
• rs4828291
• ENST00000837916.1:n.1190-31235A>G

Variant summary

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

The ENST00000837916.1(ENSG00000309030):​n.1190-31235A>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 0.88 (30328 hom., 29293 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000309030 ENST00000837916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 0 publications found

Genes affected

ENSG00000309030 (HGNC:):

ACMG classification

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

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

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
ENSG00000309030	ENST00000837916.1	n.1190-31235A>G		intron_variant	Intron 2 of 3
ENSG00000309030	ENST00000837917.1	n.231-31235A>G		intron_variant	Intron 1 of 2
ENSG00000309030	ENST00000837918.1	n.228-31235A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.884 AC: 97929 AN: 110740 Hom.: 30339 Cov.: 23

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.916

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.918

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: 0.884 AC: 97966 AN: 110795 Hom.: 30328 Cov.: 23 AF XY: 0.889 AC XY: 29293 AN XY: 32961

African (AFR) AF: 0.892 AC: 27206 AN: 30509

American (AMR) AF: 0.941 AC: 9769 AN: 10384

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 2432 AN: 2647

East Asian (EAS) AF: 0.988 AC: 3475 AN: 3518

South Asian (SAS) AF: 0.896 AC: 2302 AN: 2569

European-Finnish (FIN) AF: 0.890 AC: 5247 AN: 5897

Middle Eastern (MID) AF: 0.903 AC: 195 AN: 216

European-Non Finnish (NFE) AF: 0.860 AC: 45469 AN: 52887

Other (OTH) AF: 0.913 AC: 1360 AN: 1489

Alfa AF: 0.867 Hom.: 42864

Bravo AF: 0.889

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.70
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4828291; hg19: chrX-84025957;