X-148161331-T-G

Variant names:

• chrX-148161331-T-G
• rs1990383
• ENST00000821191.1:n.463+31852T>G

Variant summary

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

The ENST00000821191.1(ENSG00000306798):​n.463+31852T>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 0.74 (21715 hom., 23462 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000306798 ENST00000821191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 5 publications found

Genes affected

ENSG00000306798 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821191.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306798	ENST00000821191.1		n.463+31852T>G		intron	N/A
	ENSG00000306798	ENST00000821192.1		n.221+31852T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.743 AC: 81311 AN: 109457 Hom.: 21708 Cov.: 22

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.736

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: 0.743 AC: 81349 AN: 109507 Hom.: 21715 Cov.: 22 AF XY: 0.738 AC XY: 23462 AN XY: 31805

African (AFR) AF: 0.793 AC: 23887 AN: 30105

American (AMR) AF: 0.774 AC: 7910 AN: 10214

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 1542 AN: 2610

East Asian (EAS) AF: 0.828 AC: 2835 AN: 3423

South Asian (SAS) AF: 0.626 AC: 1578 AN: 2519

European-Finnish (FIN) AF: 0.680 AC: 3876 AN: 5704

Middle Eastern (MID) AF: 0.700 AC: 152 AN: 217

European-Non Finnish (NFE) AF: 0.721 AC: 37897 AN: 52538

Other (OTH) AF: 0.738 AC: 1105 AN: 1497

Alfa AF: 0.736 Hom.: 82445

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.56
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1990383;

hg19: chrX-147242851;