2-129276439-C-A

Variant names:

• chr2-129276439-C-A
• rs837841
• XR_007087234.1:n.277-12511C>A

Variant summary

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

The XR_007087234.1(LOC105373612):​n.277-12511C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,968 control chromosomes in the GnomAD database, including 14,644 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 0.43 (14644 hom., cov: 33)
• Consequence: LOC105373612 XR_007087234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 8 publications found

Genes affected

LOC105373612 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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: 0.431 AC: 65521 AN: 151852 Hom.: 14622 Cov.: 33

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.432 AC: 65586 AN: 151968 Hom.: 14644 Cov.: 33 AF XY: 0.435 AC XY: 32305 AN XY: 74286

African (AFR) AF: 0.489 AC: 20243 AN: 41428

American (AMR) AF: 0.526 AC: 8026 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3585 AN: 5152

South Asian (SAS) AF: 0.451 AC: 2172 AN: 4816

European-Finnish (FIN) AF: 0.384 AC: 4055 AN: 10570

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25372 AN: 67960

Other (OTH) AF: 0.405 AC: 853 AN: 2106

Alfa AF: 0.397 Hom.: 18645

Bravo AF: 0.449

Asia WGS AF: 0.583 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.32
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs837841; hg19: chr2-130034012;