11-113496845-C-T

Variant names:

• chr11-113496845-C-T
• rs10736466
• XR_948024.2:n.106+3793G>A

Variant summary

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

The XR_948024.2(LOC105369501):​n.106+3793G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,746 control chromosomes in the GnomAD database, including 17,853 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 (17853 hom., cov: 30)
• Consequence: LOC105369501 XR_948024.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.96
• Publications: 2 publications found

Genes affected

LOC105369501 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 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: 0.452 AC: 68491 AN: 151628 Hom.: 17806 Cov.: 30

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.452 AC: 68603 AN: 151746 Hom.: 17853 Cov.: 30 AF XY: 0.454 AC XY: 33687 AN XY: 74152

African (AFR) AF: 0.701 AC: 29012 AN: 41404

American (AMR) AF: 0.476 AC: 7261 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3472

East Asian (EAS) AF: 0.693 AC: 3546 AN: 5120

South Asian (SAS) AF: 0.381 AC: 1829 AN: 4796

European-Finnish (FIN) AF: 0.375 AC: 3941 AN: 10512

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20650 AN: 67878

Other (OTH) AF: 0.400 AC: 842 AN: 2104

Alfa AF: 0.308 Hom.: 4134

Bravo AF: 0.472

Asia WGS AF: 0.555 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.017
DANN	Benign	0.72
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs10736466; hg19: chr11-113367567;