12-94509493-G-C

Variant names:

• chr12-94509493-G-C
• rs10507038
• XR_945224.3:n.215-29395G>C

Variant summary

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

The XR_945224.3(LOC102724960):​n.215-29395G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,948 control chromosomes in the GnomAD database, including 19,582 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 0.50 (19582 hom., cov: 31)
• Consequence: LOC102724960 XR_945224.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 0 publications found

Genes affected

LOC102724960 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 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: 0.498 AC: 75597 AN: 151830 Hom.: 19584 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.498 AC: 75606 AN: 151948 Hom.: 19582 Cov.: 31 AF XY: 0.492 AC XY: 36544 AN XY: 74246

African (AFR) AF: 0.380 AC: 15758 AN: 41448

American (AMR) AF: 0.488 AC: 7458 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1362 AN: 5170

South Asian (SAS) AF: 0.383 AC: 1840 AN: 4810

European-Finnish (FIN) AF: 0.506 AC: 5326 AN: 10520

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40148 AN: 67948

Other (OTH) AF: 0.530 AC: 1119 AN: 2112

Alfa AF: 0.403 Hom.: 1135

Bravo AF: 0.491

Asia WGS AF: 0.299 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.2
DANN	Benign	0.76
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10507038; hg19: chr12-94903269;