9-114563056-A-G

Variant names:

• chr9-114563056-A-G
• rs7851259
• XR_930260.2:n.200+1312T>C

Variant summary

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

The XR_930260.2(LOC105376229):​n.200+1312T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,094 control chromosomes in the GnomAD database, including 16,824 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 0.47 (16824 hom., cov: 33)
• Consequence: LOC105376229 XR_930260.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 3 publications found

Genes affected

LOC105376229 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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: 0.469 AC: 71244 AN: 151976 Hom.: 16817 Cov.: 33

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.469 AC: 71274 AN: 152094 Hom.: 16824 Cov.: 33 AF XY: 0.467 AC XY: 34748 AN XY: 74350

African (AFR) AF: 0.511 AC: 21196 AN: 41496

American (AMR) AF: 0.484 AC: 7391 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2108 AN: 5176

South Asian (SAS) AF: 0.495 AC: 2384 AN: 4820

European-Finnish (FIN) AF: 0.379 AC: 4004 AN: 10572

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31236 AN: 67976

Other (OTH) AF: 0.460 AC: 968 AN: 2106

Alfa AF: 0.467 Hom.: 25749

Bravo AF: 0.475

Asia WGS AF: 0.426 AC: 1477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.83
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7851259; hg19: chr9-117325336;