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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903059	XR_007063538.1	n.313-13C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;