rs10505795

Variant names:

• chr12-16183959-A-G
• rs10505795
• XR_001749028.1:n.63-15546A>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.63-15546A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 152,292 control chromosomes in the GnomAD database, including 282 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 (282 hom., cov: 32)
• Consequence: LOC101928362 XR_001749028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 2 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=-0.79).
• 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: 7013 AN: 152174 Hom.: 276 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: 0.0227

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.00574

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0237

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0463 AC: 7044 AN: 152292 Hom.: 282 Cov.: 32 AF XY: 0.0451 AC XY: 3355 AN XY: 74466

African (AFR) AF: 0.104 AC: 4309 AN: 41538

American (AMR) AF: 0.0452 AC: 692 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5180

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4826

European-Finnish (FIN) AF: 0.00574 AC: 61 AN: 10630

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

European-Non Finnish (NFE) AF: 0.0237 AC: 1610 AN: 68026

Other (OTH) AF: 0.0374 AC: 79 AN: 2114

Alfa AF: 0.0365 Hom.: 68

Bravo AF: 0.0509

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	-0.79
CADD	Benign	5.5
DANN	Benign	0.66
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs10505795; hg19: chr12-16336893;