rs12559502

Positions:

• chrX-128914567-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.2149T>C 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 0.247 in 109,738 control chromosomes in the GnomAD database, including 2,634 homozygotes. There are 7,658 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 0.25 (2634 hom., 7658 hem., cov: 22)
• Consequence: LOC124905213 XR_007068324.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

Genes affected

LOC124905213 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905213	XR_007068324.1	n.2149T>C		non_coding_transcript_exon_variant	9/9
LOC124905213	XR_007068316.1	n.6268T>C		non_coding_transcript_exon_variant	7/7
LOC124905213	XR_007068325.1	n.7677T>C		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000660383.1	n.567+117783T>C		intron_variant, non_coding_transcript_variant
	ENST00000653849.1	n.1436-79891T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.247 AC: 27095 AN: 109685 Hom.: 2634 Cov.: 22 AF XY: 0.239 AC XY: 7651 AN XY: 31965

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.247 AC: 27099 AN: 109738 Hom.: 2634 Cov.: 22 AF XY: 0.239 AC XY: 7658 AN XY: 32028

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.231

Alfa AF: 0.288 Hom.: 19458

Bravo AF: 0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.70
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12559502; hg19: chrX-128048545;