chr2-133941727-C-T

Variant names:

• chr2-133941727-C-T
• rs13388210
• XR_001739714.2:n.1936+11200G>A

Variant summary

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

The XR_001739714.2(LOC105373627):​n.1936+11200G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,966 control chromosomes in the GnomAD database, including 36,660 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 (36660 hom., cov: 31)
• Consequence: LOC105373627 XR_001739714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 3 publications found

Genes affected

LOC105373627 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 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: 0.693 AC: 105180 AN: 151848 Hom.: 36639 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.693 AC: 105258 AN: 151966 Hom.: 36660 Cov.: 31 AF XY: 0.687 AC XY: 51006 AN XY: 74280

African (AFR) AF: 0.733 AC: 30393 AN: 41476

American (AMR) AF: 0.614 AC: 9379 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2377 AN: 3466

East Asian (EAS) AF: 0.505 AC: 2606 AN: 5156

South Asian (SAS) AF: 0.614 AC: 2957 AN: 4816

European-Finnish (FIN) AF: 0.676 AC: 7145 AN: 10568

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48166 AN: 67906

Other (OTH) AF: 0.682 AC: 1440 AN: 2112

Alfa AF: 0.653 Hom.: 3663

Bravo AF: 0.691

Asia WGS AF: 0.584 AC: 2029 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.50
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs13388210; hg19: chr2-134699298;