9-114561146-T-C

Variant names:

• chr9-114561146-T-C
• rs4979427
• XR_930260.2:n.201-2405A>G

Variant summary

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

The XR_930260.2(LOC105376229):​n.201-2405A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,108 control chromosomes in the GnomAD database, including 8,591 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 0.33 (8591 hom., cov: 32)
• Consequence: LOC105376229 XR_930260.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 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: 0.329 AC: 50067 AN: 151990 Hom.: 8564 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.330 AC: 50149 AN: 152108 Hom.: 8591 Cov.: 32 AF XY: 0.329 AC XY: 24469 AN XY: 74352

African (AFR) AF: 0.379 AC: 15737 AN: 41476

American (AMR) AF: 0.324 AC: 4954 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1059 AN: 3466

East Asian (EAS) AF: 0.545 AC: 2818 AN: 5170

South Asian (SAS) AF: 0.306 AC: 1479 AN: 4826

European-Finnish (FIN) AF: 0.322 AC: 3406 AN: 10586

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

European-Non Finnish (NFE) AF: 0.286 AC: 19426 AN: 67992

Other (OTH) AF: 0.327 AC: 690 AN: 2110

Alfa AF: 0.299 Hom.: 11864

Bravo AF: 0.337

Asia WGS AF: 0.437 AC: 1522 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	0.21
DANN	Benign	0.54
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4979427; hg19: chr9-117323426;