9-108150525-G-C

Variant names:

• chr9-108150525-G-C
• rs633082
• XR_001746881.2:n.721-97231C>G

Variant summary

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

The XR_001746881.2(LOC105376214):​n.721-97231C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,962 control chromosomes in the GnomAD database, including 6,580 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 0.29 (6580 hom., cov: 33)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.448 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: 0.293 AC: 44426 AN: 151844 Hom.: 6570 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.293 AC: 44465 AN: 151962 Hom.: 6580 Cov.: 33 AF XY: 0.300 AC XY: 22249 AN XY: 74252

African (AFR) AF: 0.290 AC: 12034 AN: 41436

American (AMR) AF: 0.236 AC: 3609 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2389 AN: 5156

South Asian (SAS) AF: 0.388 AC: 1869 AN: 4816

European-Finnish (FIN) AF: 0.333 AC: 3509 AN: 10526

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.281 AC: 19088 AN: 67974

Other (OTH) AF: 0.276 AC: 584 AN: 2114

Alfa AF: 0.170 Hom.: 330

Bravo AF: 0.285

Asia WGS AF: 0.379 AC: 1319 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	1.2
DANN	Benign	0.66
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs633082; hg19: chr9-110912805;