X-140538395-G-A

Variant names:

• chrX-140538395-G-A
• rs203648
• ENST00000797998.1:n.312+19551G>A

Variant summary

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

The ENST00000797998.1(ENSG00000303910):​n.312+19551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 110,811 control chromosomes in the GnomAD database, including 5,950 homozygotes. There are 11,256 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 0.35 (5950 hom., 11256 hem., cov: 22)
• Consequence: ENSG00000303910 ENST00000797998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 2 publications found

Genes affected

ENSG00000303910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797998.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303910	ENST00000797998.1		n.312+19551G>A		intron	N/A
	ENSG00000303910	ENST00000797999.1		n.476+4875G>A		intron	N/A
	ENSG00000303910	ENST00000798000.1		n.367+4875G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.349 AC: 38690 AN: 110754 Hom.: 5950 Cov.: 22

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.349 AC: 38690 AN: 110811 Hom.: 5950 Cov.: 22 AF XY: 0.340 AC XY: 11256 AN XY: 33067

African (AFR) AF: 0.0866 AC: 2657 AN: 30675

American (AMR) AF: 0.447 AC: 4663 AN: 10431

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1191 AN: 2627

East Asian (EAS) AF: 0.567 AC: 1960 AN: 3457

South Asian (SAS) AF: 0.383 AC: 998 AN: 2607

European-Finnish (FIN) AF: 0.344 AC: 2013 AN: 5844

Middle Eastern (MID) AF: 0.509 AC: 111 AN: 218

European-Non Finnish (NFE) AF: 0.459 AC: 24228 AN: 52758

Other (OTH) AF: 0.393 AC: 595 AN: 1515

Alfa AF: 0.266 Hom.: 3014

Bravo AF: 0.351

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.79
DANN	Benign	0.64
PhyloP100		0.053

Splicing

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

Other links and lift over

dbSNP: rs203648; hg19: chrX-139620560;