11-106393118-C-G

Variant names:

• chr11-106393118-C-G
• rs1606328
• XR_947985.1:n.102-16025C>G

Variant summary

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

The XR_947985.1(LOC105369474):​n.102-16025C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,038 control chromosomes in the GnomAD database, including 37,004 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 0.69 (37004 hom., cov: 31)
• Consequence: LOC105369474 XR_947985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 1 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 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: 0.695 AC: 105546 AN: 151920 Hom.: 36980 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.695 AC: 105609 AN: 152038 Hom.: 37004 Cov.: 31 AF XY: 0.693 AC XY: 51490 AN XY: 74282

African (AFR) AF: 0.799 AC: 33143 AN: 41490

American (AMR) AF: 0.574 AC: 8770 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2037 AN: 3466

East Asian (EAS) AF: 0.641 AC: 3303 AN: 5154

South Asian (SAS) AF: 0.649 AC: 3131 AN: 4824

European-Finnish (FIN) AF: 0.693 AC: 7317 AN: 10564

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45687 AN: 67962

Other (OTH) AF: 0.656 AC: 1384 AN: 2110

Alfa AF: 0.688 Hom.: 4496

Bravo AF: 0.686

Asia WGS AF: 0.620 AC: 2156 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	2.3
DANN	Benign	0.42
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1606328; hg19: chr11-106263845;