chr2-105352399-C-G

Position:

• chr2-105352399-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047445805.1(C2orf49):​c.*18+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 XM_047445805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2orf49	XM_047445805.1	c.*18+7010C>G		intron_variant			XP_047301761.1
C2orf49	XM_017004892.3	c.*18+7010C>G		intron_variant			XP_016860381.2
		n.105352399C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.142

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2576773; hg19: chr2-105968856;