rs12559502

Variant names:

• chrX-128914567-A-G
• rs12559502
• XR_007068316.1:n.6268T>C

Variant summary

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

The XR_007068316.1(LOC124905213):​n.6268T>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_007068316.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 0 publications found

Genes affected

LOC124905213 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124905213	XR_007068316.1	n.6268T>C		non_coding_transcript_exon_variant	Exon 7 of 7
LOC124905213	XR_007068324.1	n.2149T>C		non_coding_transcript_exon_variant	Exon 9 of 9
LOC124905213	XR_007068325.1	n.7677T>C		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225689	ENST00000653849.1	n.1436-79891T>C		intron_variant	Intron 6 of 6
ENSG00000225689	ENST00000660383.1	n.567+117783T>C		intron_variant	Intron 5 of 10

Frequencies

GnomAD3 genomes AF: 0.247 AC: 27095 AN: 109685 Hom.: 2634 Cov.: 22

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

African (AFR) AF: 0.162 AC: 4903 AN: 30264

American (AMR) AF: 0.200 AC: 2053 AN: 10245

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 737 AN: 2624

East Asian (EAS) AF: 0.189 AC: 652 AN: 3446

South Asian (SAS) AF: 0.195 AC: 487 AN: 2495

European-Finnish (FIN) AF: 0.350 AC: 1993 AN: 5700

Middle Eastern (MID) AF: 0.234 AC: 50 AN: 214

European-Non Finnish (NFE) AF: 0.298 AC: 15672 AN: 52584

Other (OTH) AF: 0.231 AC: 346 AN: 1495

Alfa AF: 0.274 Hom.: 25206

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs12559502; hg19: chrX-128048545;