rs7889974

Positions:

• chrX-142077257-A-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, non coding transcript 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: ENST00000664519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664519.1	n.223-118450A>G		intron_variant, non_coding_transcript_variant

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;