rs1359076

Variant names:

• chr9-108283554-C-T
• rs1359076
• XR_001746881.2:n.720+27112G>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.720+27112G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,156 control chromosomes in the GnomAD database, including 2,775 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 0.12 (2775 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 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: 0.116 AC: 17620 AN: 152038 Hom.: 2771 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.00594

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0166

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.116 AC: 17644 AN: 152156 Hom.: 2775 Cov.: 32 AF XY: 0.112 AC XY: 8364 AN XY: 74400

African (AFR) AF: 0.357 AC: 14791 AN: 41466

American (AMR) AF: 0.0578 AC: 884 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.0215 AC: 111 AN: 5170

South Asian (SAS) AF: 0.0364 AC: 176 AN: 4830

European-Finnish (FIN) AF: 0.00594 AC: 63 AN: 10614

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0166 AC: 1126 AN: 68002

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.0648 Hom.: 1953

Bravo AF: 0.128

Asia WGS AF: 0.0460 AC: 159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1359076; hg19: chr9-111045834;