rs11706236

Variant names:

• chr3-55154246-A-G
• rs11706236
• XR_007095917.1:n.159-10324T>C

Variant summary

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

The XR_007095917.1(LOC124906243):​n.159-10324T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,182 control chromosomes in the GnomAD database, including 1,001 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 0.10 (1001 hom., cov: 32)
• Consequence: LOC124906243 XR_007095917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 5 publications found

Genes affected

LOC124906243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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: 0.100 AC: 15272 AN: 152064 Hom.: 1000 Cov.: 32

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0938

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.100 AC: 15275 AN: 152182 Hom.: 1001 Cov.: 32 AF XY: 0.0991 AC XY: 7371 AN XY: 74392

African (AFR) AF: 0.0308 AC: 1281 AN: 41546

American (AMR) AF: 0.0664 AC: 1016 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0938 AC: 325 AN: 3466

East Asian (EAS) AF: 0.0700 AC: 361 AN: 5160

South Asian (SAS) AF: 0.0664 AC: 320 AN: 4818

European-Finnish (FIN) AF: 0.168 AC: 1783 AN: 10584

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9624 AN: 67996

Other (OTH) AF: 0.0969 AC: 205 AN: 2116

Alfa AF: 0.124 Hom.: 2358

Bravo AF: 0.0912

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.7
DANN	Benign	0.78
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs11706236; hg19: chr3-55188273;