12-10536155-C-G

Variant names:

• chr12-10536155-C-G
• rs10845158
• XR_001749003.3:n.31+914G>C

Variant summary

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

The XR_931355.4(LOC105369657):​n.31+914G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,598 control chromosomes in the GnomAD database, including 5,908 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 0.25 (5908 hom., cov: 32)
• Consequence: LOC105369657 XR_931355.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 2 publications found

Genes affected

LOC105369657 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38499 AN: 151480 Hom.: 5891 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.254 AC: 38532 AN: 151598 Hom.: 5908 Cov.: 32 AF XY: 0.260 AC XY: 19271 AN XY: 74046

African (AFR) AF: 0.125 AC: 5172 AN: 41388

American (AMR) AF: 0.378 AC: 5755 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3466

East Asian (EAS) AF: 0.690 AC: 3561 AN: 5162

South Asian (SAS) AF: 0.326 AC: 1565 AN: 4804

European-Finnish (FIN) AF: 0.254 AC: 2646 AN: 10412

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.265 AC: 17950 AN: 67834

Other (OTH) AF: 0.268 AC: 565 AN: 2106

Alfa AF: 0.237 Hom.: 578

Bravo AF: 0.263

Asia WGS AF: 0.480 AC: 1669 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.37
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs10845158; hg19: chr12-10688754;