chrX-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).

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
ENSG00000306798	ENST00000821191.1	n.463+31852T>G		intron_variant	Intron 1 of 2
ENSG00000306798	ENST00000821192.1	n.221+31852T>G		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs1990383; hg19: chrX-147242851;