X-129134974-A-G

Position:

• chrX-129134974-A-G

Variant summary

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

The XR_007068324.1(LOC124905213):​n.1012-12781T>C 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 0.276 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: LOC124905213 XR_007068324.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816

Genes affected

LOC124905213 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124905213	XR_007068324.1	n.1012-12781T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653849.1	n.1101-12781T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.275 AC: 30510 AN: 110789 Hom.: 4563 Cov.: 23 AF XY: 0.256 AC XY: 8462 AN XY: 33075

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

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.277

Alfa AF: 0.191 Hom.: 3447

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5975081; hg19: chrX-128268951;