chrX-151534009-T-A

Variant names:

• chrX-151534009-T-A
• rs7051678
• ENST00000811741.1:n.44-1533A>T

Variant summary

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

The NR_188661.1(LOC105373367):​n.229-1533A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 111,872 control chromosomes in the GnomAD database, including 1,030 homozygotes. There are 3,306 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 0.11 (1030 hom., 3306 hem., cov: 23)
• Consequence: LOC105373367 NR_188661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.933
• Publications: 1 publications found

Genes affected

ENSG00000305574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188661.1. 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
	LOC105373367	NR_188661.1		n.229-1533A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305574	ENST00000811741.1		n.44-1533A>T		intron	N/A
	ENSG00000305574	ENST00000811742.1		n.450-1533A>T		intron	N/A
	ENSG00000305574	ENST00000811743.1		n.97-1533A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 12109 AN: 111821 Hom.: 1029 Cov.: 23

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0397

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.0627

Gnomad EAS AF: 0.00927

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0158

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0396

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.108 AC: 12121 AN: 111872 Hom.: 1030 Cov.: 23 AF XY: 0.0970 AC XY: 3306 AN XY: 34090

African (AFR) AF: 0.286 AC: 8768 AN: 30656

American (AMR) AF: 0.0597 AC: 631 AN: 10569

Ashkenazi Jewish (ASJ) AF: 0.0627 AC: 166 AN: 2648

East Asian (EAS) AF: 0.00930 AC: 33 AN: 3549

South Asian (SAS) AF: 0.0454 AC: 121 AN: 2667

European-Finnish (FIN) AF: 0.0158 AC: 97 AN: 6124

Middle Eastern (MID) AF: 0.0558 AC: 12 AN: 215

European-Non Finnish (NFE) AF: 0.0395 AC: 2105 AN: 53235

Other (OTH) AF: 0.105 AC: 161 AN: 1529

Alfa AF: 0.00623 Hom.: 28

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.70
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs7051678; hg19: chrX-150702481;