chr3-63827978-A-C

Position:

• chr3-63827978-A-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001355236.2(C3orf49):​c.570+253A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,002 control chromosomes in the GnomAD database, including 1,910 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 0.15 (1910 hom., cov: 32)
• Consequence: C3orf49 NM_001355236.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620

Genes affected

C3orf49 (HGNC:25190): (chromosome 3 open reading frame 49)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C3orf49	NM_001355236.2	c.570+253A>C		intron_variant		ENST00000295896.13
C3orf49	XM_024453353.2	c.570+253A>C		intron_variant
C3orf49	XM_047447470.1	c.366+253A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C3orf49	ENST00000295896.13	c.570+253A>C		intron_variant		2	NM_001355236.2	A2
C3orf49	ENST00000491896.1	c.195+253A>C		intron_variant		2
C3orf49	ENST00000647022.1	c.570+253A>C		intron_variant				P2
C3orf49	ENST00000673037.1	c.437+253A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23029 AN: 151884 Hom.: 1909 Cov.: 32

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.152 AC: 23038 AN: 152002 Hom.: 1910 Cov.: 32 AF XY: 0.150 AC XY: 11136 AN XY: 74316

Gnomad4 AFR AF: 0.0813

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.171

Alfa AF: 0.186 Hom.: 4052

Bravo AF: 0.154

Asia WGS AF: 0.114 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	20
DANN	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.33		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.33		Position offset: 16

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

Publications

LitVar

Other links and lift over

dbSNP: rs7614311; hg19: chr3-63813654;