chr11-106391670-C-T

Variant names:

• chr11-106391670-C-T
• rs567992
• XR_947985.1:n.102-17473C>T

Variant summary

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

The XR_947985.1(LOC105369474):​n.102-17473C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,100 control chromosomes in the GnomAD database, including 1,816 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 0.13 (1816 hom., cov: 32)
• Consequence: LOC105369474 XR_947985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 5 publications found

Genes affected

LOC105369474 (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 (AMR) allele frequency at 95% confidence interval = 0.282 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: 0.130 AC: 19760 AN: 151982 Hom.: 1807 Cov.: 32

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.130 AC: 19777 AN: 152100 Hom.: 1816 Cov.: 32 AF XY: 0.136 AC XY: 10077 AN XY: 74332

African (AFR) AF: 0.0288 AC: 1197 AN: 41516

American (AMR) AF: 0.289 AC: 4407 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3470

East Asian (EAS) AF: 0.233 AC: 1199 AN: 5148

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4818

European-Finnish (FIN) AF: 0.152 AC: 1603 AN: 10574

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9437 AN: 67992

Other (OTH) AF: 0.155 AC: 328 AN: 2112

Alfa AF: 0.140 Hom.: 3677

Bravo AF: 0.137

Asia WGS AF: 0.200 AC: 697 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	0.32
DANN	Benign	0.65
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs567992; hg19: chr11-106262397;