rs1243792

Variant names:

• chrX-41012314-G-A
• rs1243792
• ENST00000661498.1:n.143-3069C>T

Variant summary

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

The ENST00000661498.1(ENSG00000287549):​n.143-3069C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 109,656 control chromosomes in the GnomAD database, including 7,314 homozygotes. There are 13,419 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 0.43 (7314 hom., 13419 hem., cov: 21)
• Consequence: ENSG00000287549 ENST00000661498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 publications found

Genes affected

ENSG00000287549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 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
ENSG00000287549	ENST00000661498.1	n.143-3069C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 46719 AN: 109601 Hom.: 7324 Cov.: 21

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.426 AC: 46713 AN: 109656 Hom.: 7314 Cov.: 21 AF XY: 0.419 AC XY: 13419 AN XY: 32014

African (AFR) AF: 0.343 AC: 10364 AN: 30240

American (AMR) AF: 0.400 AC: 4109 AN: 10260

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1136 AN: 2629

East Asian (EAS) AF: 0.395 AC: 1357 AN: 3434

South Asian (SAS) AF: 0.547 AC: 1397 AN: 2553

European-Finnish (FIN) AF: 0.479 AC: 2743 AN: 5721

Middle Eastern (MID) AF: 0.495 AC: 105 AN: 212

European-Non Finnish (NFE) AF: 0.469 AC: 24592 AN: 52447

Other (OTH) AF: 0.430 AC: 640 AN: 1489

Alfa AF: 0.455 Hom.: 55667

Bravo AF: 0.416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.1
DANN	Benign	0.26
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1243792; hg19: chrX-40871567;