chr9-108150874-T-G

Variant names:

• chr9-108150874-T-G
• rs634454
• XR_001746881.2:n.721-97580A>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.721-97580A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,188 control chromosomes in the GnomAD database, including 56,214 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 0.86 (56214 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 6 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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.856 AC: 130221 AN: 152070 Hom.: 56149 Cov.: 32

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.856 AC: 130343 AN: 152188 Hom.: 56214 Cov.: 32 AF XY: 0.863 AC XY: 64234 AN XY: 74388

African (AFR) AF: 0.941 AC: 39113 AN: 41544

American (AMR) AF: 0.862 AC: 13194 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2559 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5151 AN: 5158

South Asian (SAS) AF: 0.926 AC: 4463 AN: 4818

European-Finnish (FIN) AF: 0.865 AC: 9163 AN: 10590

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53886 AN: 67990

Other (OTH) AF: 0.829 AC: 1752 AN: 2114

Alfa AF: 0.835 Hom.: 36925

Bravo AF: 0.859

Asia WGS AF: 0.964 AC: 3353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	14
DANN	Benign	0.74
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs634454; hg19: chr9-110913154;