rs7889974

Variant names:

• chrX-142077257-A-G
• rs7889974
• ENST00000664519.1:n.223-118450A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664519.1(ENSG00000288098):​n.223-118450A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 111,767 control chromosomes in the GnomAD database, including 1,211 homozygotes. There are 4,560 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 0.15 (1211 hom., 4560 hem., cov: 24)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 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
ENSG00000288098	ENST00000664519.1	n.223-118450A>G		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.154 AC: 17179 AN: 111711 Hom.: 1210 Cov.: 24 AF XY: 0.134 AC XY: 4552 AN XY: 33915

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0878

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.000282

Gnomad SAS AF: 0.0299

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.154 AC: 17191 AN: 111767 Hom.: 1211 Cov.: 24 AF XY: 0.134 AC XY: 4560 AN XY: 33981

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.000283

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.0723

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.177

Alfa AF: 0.138 Hom.: 2525

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0080
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7889974; hg19: chrX-141165043;