XR_007063538.1:n.313-13C>G

Variant names:

• chr12-131893588-G-C
• rs10902469
• XR_007063538.1:n.313-13C>G

Variant summary

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

The XR_007063538.1(LOC124903059):​n.313-13C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,108 control chromosomes in the GnomAD database, including 4,634 homozygotes. 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 0.17 (4634 hom., cov: 32)
• Consequence: LOC124903059 XR_007063538.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 8 publications found

Genes affected

LOC124903059 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26511 AN: 151990 Hom.: 4628 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0731

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0578

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.175 AC: 26544 AN: 152108 Hom.: 4634 Cov.: 32 AF XY: 0.173 AC XY: 12851 AN XY: 74378

African (AFR) AF: 0.449 AC: 18599 AN: 41418

American (AMR) AF: 0.0956 AC: 1461 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.0731 AC: 379 AN: 5184

South Asian (SAS) AF: 0.118 AC: 567 AN: 4824

European-Finnish (FIN) AF: 0.0693 AC: 734 AN: 10598

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0579 AC: 3936 AN: 68018

Other (OTH) AF: 0.149 AC: 314 AN: 2114

Alfa AF: 0.0455 Hom.: 91

Bravo AF: 0.188

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.65
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10902469; hg19: chr12-132378133;