rs7889321

Variant names:

• chrX-50932928-A-G
• rs7889321
• ENST00000729211.1:n.236-1095T>C

Variant summary

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

The ENST00000729211.1(ENSG00000295312):​n.236-1095T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 111,227 control chromosomes in the GnomAD database, including 2,717 homozygotes. There are 5,070 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 0.17 (2717 hom., 5070 hem., cov: 23)
• Consequence: ENSG00000295312 ENST00000729211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 0 publications found

Genes affected

ENSG00000295312 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729211.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295312	ENST00000729211.1		n.236-1095T>C		intron	N/A
	ENSG00000295312	ENST00000729212.1		n.582+687T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 18423 AN: 111171 Hom.: 2715 Cov.: 23

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.0261

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0508

Gnomad EAS AF: 0.0653

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0130

Gnomad MID AF: 0.0932

Gnomad NFE AF: 0.0390

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.166 AC: 18436 AN: 111227 Hom.: 2717 Cov.: 23 AF XY: 0.151 AC XY: 5070 AN XY: 33485

African (AFR) AF: 0.478 AC: 14496 AN: 30340

American (AMR) AF: 0.0810 AC: 851 AN: 10506

Ashkenazi Jewish (ASJ) AF: 0.0508 AC: 134 AN: 2640

East Asian (EAS) AF: 0.0647 AC: 227 AN: 3511

South Asian (SAS) AF: 0.126 AC: 334 AN: 2643

European-Finnish (FIN) AF: 0.0130 AC: 79 AN: 6072

Middle Eastern (MID) AF: 0.0977 AC: 21 AN: 215

European-Non Finnish (NFE) AF: 0.0390 AC: 2073 AN: 53103

Other (OTH) AF: 0.135 AC: 203 AN: 1508

Alfa AF: 0.0979 Hom.: 3938

Bravo AF: 0.186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7889321; hg19: chrX-50675928;