rs10505796

Variant names:

• chr12-16184334-C-G
• rs10505796
• XR_001749028.1:n.63-15171C>G

Variant summary

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

The XR_001749028.1(LOC101928362):​n.63-15171C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0462 in 152,180 control chromosomes in the GnomAD database, including 280 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 0.046 (280 hom., cov: 32)
• Consequence: LOC101928362 XR_001749028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788
• Publications: 1 publications found

Genes affected

LOC101928362 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 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: 0.0461 AC: 7005 AN: 152062 Hom.: 274 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0454

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0228

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.00566

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0238

Gnomad OTH AF: 0.0377

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

GnomAD4 genome AF: 0.0462 AC: 7036 AN: 152180 Hom.: 280 Cov.: 32 AF XY: 0.0450 AC XY: 3349 AN XY: 74396

African (AFR) AF: 0.104 AC: 4298 AN: 41506

American (AMR) AF: 0.0452 AC: 691 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3466

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5170

South Asian (SAS) AF: 0.0249 AC: 120 AN: 4820

European-Finnish (FIN) AF: 0.00566 AC: 60 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0238 AC: 1617 AN: 68010

Other (OTH) AF: 0.0373 AC: 79 AN: 2116

Alfa AF: 0.0355 Hom.: 30

Bravo AF: 0.0510

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.37
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10505796; hg19: chr12-16337268;