rs12358485

Variant names:

• chr10-57769013-C-T
• rs12358485
• XR_001747454.1:n.86-67628G>A

Variant summary

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

The XR_001747454.1(LOC105378314):​n.86-67628G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 151,864 control chromosomes in the GnomAD database, including 49,615 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 0.80 (49615 hom., cov: 32)
• Consequence: LOC105378314 XR_001747454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 1 publications found

Genes affected

LOC105378314 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 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: 0.805 AC: 122088 AN: 151746 Hom.: 49603 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.804 AC: 122138 AN: 151864 Hom.: 49615 Cov.: 32 AF XY: 0.800 AC XY: 59382 AN XY: 74204

African (AFR) AF: 0.712 AC: 29520 AN: 41438

American (AMR) AF: 0.851 AC: 12937 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3165 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3671 AN: 5150

South Asian (SAS) AF: 0.606 AC: 2917 AN: 4814

European-Finnish (FIN) AF: 0.830 AC: 8785 AN: 10580

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58319 AN: 67894

Other (OTH) AF: 0.825 AC: 1739 AN: 2108

Alfa AF: 0.826 Hom.: 6769

Bravo AF: 0.809

Asia WGS AF: 0.630 AC: 2193 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.35
DANN	Benign	0.23
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12358485; hg19: chr10-59528773;