rs13295552

Variant names:

• chr9-81907834-A-C
• rs13295552
• NR_188610.1:n.1326-19929T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_188610.1(LOC105376105):​n.1326-19929T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 152,240 control chromosomes in the GnomAD database, including 47 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 0.021 (47 hom., cov: 33)
• Consequence: LOC105376105 NR_188610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 3 publications found

Genes affected

LOC105376105 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0214 (3263/152240) while in subpopulation NFE AF = 0.0309 (2101/68022). AF 95% confidence interval is 0.0298. There are 47 homozygotes in GnomAd4. There are 1559 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 47 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188610.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105376105	NR_188610.1		n.1326-19929T>G		intron	N/A
	LOC105376105	NR_188611.1		n.1515-19929T>G		intron	N/A

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: 0.0214 AC: 3263 AN: 152122 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.00635

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.0366

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0214 AC: 3263 AN: 152240 Hom.: 47 Cov.: 33 AF XY: 0.0209 AC XY: 1559 AN XY: 74436

African (AFR) AF: 0.00633 AC: 263 AN: 41534

American (AMR) AF: 0.0222 AC: 339 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.00207 AC: 10 AN: 4828

European-Finnish (FIN) AF: 0.0366 AC: 388 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0309 AC: 2101 AN: 68022

Other (OTH) AF: 0.0289 AC: 61 AN: 2110

Alfa AF: 0.0226 Hom.: 14

Bravo AF: 0.0201

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.76
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs13295552; hg19: chr9-84522749;