9-108292785-A-G

Variant names:

• chr9-108292785-A-G
• rs1535619
• XR_001746881.2:n.720+17881T>C

Variant summary

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

The XR_001746881.2(LOC105376214):​n.720+17881T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,010 control chromosomes in the GnomAD database, including 4,022 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 0.21 (4022 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.776
• Publications: 2 publications found

Genes affected

LOC105376214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32121 AN: 151892 Hom.: 4016 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.211 AC: 32145 AN: 152010 Hom.: 4022 Cov.: 32 AF XY: 0.211 AC XY: 15646 AN XY: 74322

African (AFR) AF: 0.338 AC: 13981 AN: 41378

American (AMR) AF: 0.196 AC: 3000 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3468

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5182

South Asian (SAS) AF: 0.139 AC: 668 AN: 4810

European-Finnish (FIN) AF: 0.197 AC: 2087 AN: 10590

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11260 AN: 67990

Other (OTH) AF: 0.184 AC: 388 AN: 2108

Alfa AF: 0.173 Hom.: 2063

Bravo AF: 0.213

Asia WGS AF: 0.0930 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.52
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs1535619; hg19: chr9-111055065;