2-105352399-C-G

Variant names:

• chr2-105352399-C-G
• rs2576773
• XM_047445805.1:c.*18+7010C>G

Variant summary

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

The XR_007081585.1(C2orf49):​n.765+7010C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 141,906 control chromosomes in the GnomAD database, including 1,767 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 0.14 (1767 hom., cov: 28)
• Consequence: C2orf49 XR_007081585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914
• Publications: 1 publications found

Genes affected

C2orf49 (HGNC:28772): (chromosome 2 open reading frame 49) Predicted to be involved in embryonic morphogenesis. Located in nucleus. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

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 (SAS) allele frequency at 95% confidence interval = 0.237 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: 0.143 AC: 20295 AN: 141892 Hom.: 1767 Cov.: 28

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0603

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.143 AC: 20299 AN: 141906 Hom.: 1767 Cov.: 28 AF XY: 0.140 AC XY: 9597 AN XY: 68362

African (AFR) AF: 0.0390 AC: 1476 AN: 37820

American (AMR) AF: 0.173 AC: 2397 AN: 13888

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 345 AN: 3406

East Asian (EAS) AF: 0.144 AC: 708 AN: 4916

South Asian (SAS) AF: 0.249 AC: 1119 AN: 4488

European-Finnish (FIN) AF: 0.127 AC: 1010 AN: 7982

Middle Eastern (MID) AF: 0.0615 AC: 16 AN: 260

European-Non Finnish (NFE) AF: 0.193 AC: 12831 AN: 66318

Other (OTH) AF: 0.142 AC: 276 AN: 1946

Alfa AF: 0.154 Hom.: 251

Bravo AF: 0.133

Asia WGS AF: 0.199 AC: 693 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	6.1
DANN	Benign	0.66
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs2576773; hg19: chr2-105968856;