chr9-108126198-G-T

Variant names:

• chr9-108126198-G-T
• rs865686
• XR_001746881.2:n.721-72904C>A

Variant summary

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

The XR_001746881.2(LOC105376214):​n.721-72904C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 151,976 control chromosomes in the GnomAD database, including 29,514 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 (29514 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 98 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 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: 0.617 AC: 93634 AN: 151858 Hom.: 29492 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.652

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: 0.617 AC: 93704 AN: 151976 Hom.: 29514 Cov.: 32 AF XY: 0.626 AC XY: 46512 AN XY: 74276

African (AFR) AF: 0.512 AC: 21203 AN: 41430

American (AMR) AF: 0.646 AC: 9869 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2192 AN: 3472

East Asian (EAS) AF: 0.929 AC: 4793 AN: 5160

South Asian (SAS) AF: 0.841 AC: 4055 AN: 4824

European-Finnish (FIN) AF: 0.660 AC: 6953 AN: 10534

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42532 AN: 67960

Other (OTH) AF: 0.629 AC: 1328 AN: 2110

Alfa AF: 0.632 Hom.: 107528

Bravo AF: 0.610

Asia WGS AF: 0.861 AC: 2991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.51
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs865686; hg19: chr9-110888478;