rs7884160

Variant names:

• chrX-126027792-A-G
• rs7884160
• ENST00000794898.1:n.202+31997T>C

Variant summary

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

The ENST00000794898.1(ENSG00000303481):​n.202+31997T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 108,633 control chromosomes in the GnomAD database, including 10,399 homozygotes. There are 13,898 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 0.46 (10399 hom., 13898 hem., cov: 21)
• Consequence: ENSG00000303481 ENST00000794898.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 1 publications found

Genes affected

ENSG00000303481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 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
ENSG00000303481	ENST00000794898.1	n.202+31997T>C		intron_variant	Intron 2 of 2
ENSG00000303481	ENST00000794899.1	n.178+31997T>C		intron_variant	Intron 2 of 2
ENSG00000303481	ENST00000794900.1	n.174+31997T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.462 AC: 50174 AN: 108583 Hom.: 10393 Cov.: 21

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.462 AC: 50221 AN: 108633 Hom.: 10399 Cov.: 21 AF XY: 0.447 AC XY: 13898 AN XY: 31117

African (AFR) AF: 0.785 AC: 23227 AN: 29589

American (AMR) AF: 0.532 AC: 5483 AN: 10314

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1014 AN: 2604

East Asian (EAS) AF: 0.503 AC: 1691 AN: 3365

South Asian (SAS) AF: 0.448 AC: 1067 AN: 2384

European-Finnish (FIN) AF: 0.254 AC: 1458 AN: 5749

Middle Eastern (MID) AF: 0.361 AC: 78 AN: 216

European-Non Finnish (NFE) AF: 0.290 AC: 15167 AN: 52272

Other (OTH) AF: 0.456 AC: 673 AN: 1476

Alfa AF: 0.384 Hom.: 2713

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7884160; hg19: chrX-125161775;