rs11049353

Variant names:

• chr12-28113890-A-G
• rs11049353
• XR_931461.3:n.103-6732T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-28113890-A-G
• chr12-28113890-A-T

Variant summary

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

The XR_931461.3(LOC105369710):​n.103-6732T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,052 control chromosomes in the GnomAD database, including 19,620 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 0.49 (19620 hom., cov: 33)
• Consequence: LOC105369710 XR_931461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 2 publications found

Genes affected

LOC105369710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 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: 0.495 AC: 75236 AN: 151934 Hom.: 19612 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.495 AC: 75256 AN: 152052 Hom.: 19620 Cov.: 33 AF XY: 0.494 AC XY: 36718 AN XY: 74310

African (AFR) AF: 0.332 AC: 13769 AN: 41506

American (AMR) AF: 0.530 AC: 8097 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2042 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3173 AN: 5164

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4820

European-Finnish (FIN) AF: 0.507 AC: 5339 AN: 10526

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38506 AN: 67964

Other (OTH) AF: 0.506 AC: 1068 AN: 2110

Alfa AF: 0.517 Hom.: 2607

Bravo AF: 0.488

Asia WGS AF: 0.500 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.12
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs11049353; hg19: chr12-28266823;