rs10979182

Variant names:

• chr9-108054739-A-G
• rs10979182
• XR_001746881.2:n.721-1445T>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.721-1445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,902 control chromosomes in the GnomAD database, including 15,733 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 0.45 (15733 hom., cov: 31)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 27 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 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: 0.446 AC: 67709 AN: 151782 Hom.: 15702 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.446 AC: 67797 AN: 151902 Hom.: 15733 Cov.: 31 AF XY: 0.456 AC XY: 33888 AN XY: 74236

African (AFR) AF: 0.398 AC: 16508 AN: 41444

American (AMR) AF: 0.598 AC: 9118 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1365 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3101 AN: 5154

South Asian (SAS) AF: 0.681 AC: 3276 AN: 4812

European-Finnish (FIN) AF: 0.472 AC: 4974 AN: 10544

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27987 AN: 67918

Other (OTH) AF: 0.458 AC: 965 AN: 2106

Alfa AF: 0.425 Hom.: 1810

Bravo AF: 0.453

Asia WGS AF: 0.643 AC: 2236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.54
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10979182; hg19: chr9-110817020;