rs7881297

Positions:

• chrX-122479066-T-G

Variant summary

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

The ENST00000687758.1(ENSG00000287776):​n.2121T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 111,305 control chromosomes in the GnomAD database, including 3,581 homozygotes. There are 5,570 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 0.18 (3581 hom., 5570 hem., cov: 23)
• Consequence: ENST00000687758.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 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
	ENST00000687758.1	n.2121T>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 20114 AN: 111254 Hom.: 3579 Cov.: 23 AF XY: 0.165 AC XY: 5539 AN XY: 33496

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.00580

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0211

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.00149

Gnomad MID AF: 0.0675

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.181 AC: 20158 AN: 111305 Hom.: 3581 Cov.: 23 AF XY: 0.166 AC XY: 5570 AN XY: 33557

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.0211

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.0762

Gnomad4 FIN AF: 0.00149

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.180

Alfa AF: 0.0457 Hom.: 2370

Bravo AF: 0.217

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.43
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7881297; hg19: chrX-121612919;