rs45631821

Variant names:

• chrX-148166786-G-A
• rs45631821
• ENST00000821191.1:n.463+37307G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000821191.1(ENSG00000306798):​n.463+37307G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0779 in 110,622 control chromosomes in the GnomAD database, including 271 homozygotes. There are 2,429 hemizygotes in GnomAD. 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 0.078 (271 hom., 2429 hem., cov: 21)
• Consequence: ENSG00000306798 ENST00000821191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 0 publications found

Genes affected

ENSG00000306798 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0915 is higher than 0.05.

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+37307G>A		intron_variant	Intron 1 of 2
ENSG00000306798	ENST00000821192.1	n.221+37307G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 8605 AN: 110578 Hom.: 271 Cov.: 21

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.0119

Gnomad AMR AF: 0.0582

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00114

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.0572

Gnomad MID AF: 0.0936

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.0976

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0779 AC: 8615 AN: 110622 Hom.: 271 Cov.: 21 AF XY: 0.0738 AC XY: 2429 AN XY: 32894

African (AFR) AF: 0.0730 AC: 2220 AN: 30405

American (AMR) AF: 0.0582 AC: 604 AN: 10386

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 283 AN: 2629

East Asian (EAS) AF: 0.00114 AC: 4 AN: 3506

South Asian (SAS) AF: 0.0163 AC: 42 AN: 2575

European-Finnish (FIN) AF: 0.0572 AC: 335 AN: 5859

Middle Eastern (MID) AF: 0.0841 AC: 18 AN: 214

European-Non Finnish (NFE) AF: 0.0937 AC: 4954 AN: 52859

Other (OTH) AF: 0.0971 AC: 147 AN: 1514

Alfa AF: 0.0813 Hom.: 467

Bravo AF: 0.0790

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.18
DANN	Benign	0.32
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs45631821; hg19: chrX-147248306;