X-129134974-A-G

Variant names:

• chrX-129134974-A-G
• rs5975081
• ENST00000782197.1:n.202A>G

Variant summary

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

The ENST00000782197.1(ENSG00000301848):​n.202A>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 0.276 in 110,846 control chromosomes in the GnomAD database, including 4,571 homozygotes. There are 8,499 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 0.28 (4571 hom., 8499 hem., cov: 23)
• Consequence: ENSG00000301848 ENST00000782197.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816
• Publications: 1 publications found

Genes affected

ENSG00000301848 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905213	XR_007068324.1	n.1012-12781T>C		intron_variant	Intron 3 of 8
LOC124905213	XR_007068325.1	n.-172T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301848	ENST00000782197.1	n.202A>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000225689	ENST00000653849.1	n.1101-12781T>C		intron_variant	Intron 3 of 6
ENSG00000301792	ENST00000781917.1	n.49-15165A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 30510 AN: 110789 Hom.: 4563 Cov.: 23

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.0496

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.276 AC: 30566 AN: 110846 Hom.: 4571 Cov.: 23 AF XY: 0.256 AC XY: 8499 AN XY: 33142

African (AFR) AF: 0.571 AC: 17285 AN: 30275

American (AMR) AF: 0.252 AC: 2623 AN: 10417

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 213 AN: 2640

East Asian (EAS) AF: 0.218 AC: 770 AN: 3525

South Asian (SAS) AF: 0.177 AC: 468 AN: 2637

European-Finnish (FIN) AF: 0.102 AC: 614 AN: 5995

Middle Eastern (MID) AF: 0.245 AC: 52 AN: 212

European-Non Finnish (NFE) AF: 0.153 AC: 8086 AN: 52942

Other (OTH) AF: 0.277 AC: 421 AN: 1518

Alfa AF: 0.188 Hom.: 3793

Bravo AF: 0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs5975081; hg19: chrX-128268951;