9-108125716-C-G

Variant names:

• chr9-108125716-C-G
• rs662694
• XR_001746881.2:n.721-72422G>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.721-72422G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,968 control chromosomes in the GnomAD database, including 29,485 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 0.62 (29485 hom., cov: 31)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 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: 0.616 AC: 93562 AN: 151850 Hom.: 29465 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.616 AC: 93631 AN: 151968 Hom.: 29485 Cov.: 31 AF XY: 0.626 AC XY: 46484 AN XY: 74282

African (AFR) AF: 0.511 AC: 21167 AN: 41404

American (AMR) AF: 0.644 AC: 9849 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4798 AN: 5168

South Asian (SAS) AF: 0.839 AC: 4042 AN: 4816

European-Finnish (FIN) AF: 0.660 AC: 6951 AN: 10530

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42524 AN: 67964

Other (OTH) AF: 0.629 AC: 1330 AN: 2116

Alfa AF: 0.624 Hom.: 3760

Bravo AF: 0.609

Asia WGS AF: 0.861 AC: 2990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.55
DANN	Benign	0.39
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs662694; hg19: chr9-110887996; COSMIC: COSV60389973;