rs7651825

Positions:

• chr3-14770611-G-A
• chr3-14770611-G-C

Variant summary

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

The NM_032137.5(C3orf20):​c.2496-1456G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,854 control chromosomes in the GnomAD database, including 9,200 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 0.32 (9200 hom., cov: 31)
• Consequence: C3orf20 NM_032137.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

Genes affected

C3orf20 (HGNC:25320): (chromosome 3 open reading frame 20) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C3orf20	NM_032137.5	c.2496-1456G>A		intron_variant		ENST00000253697.8	NP_115513.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C3orf20	ENST00000253697.8	c.2496-1456G>A		intron_variant		1	NM_032137.5	ENSP00000253697.3
C3orf20	ENST00000412910.1	c.2130-1456G>A		intron_variant		1		ENSP00000396081.1
C3orf20	ENST00000435614.5	c.2130-1456G>A		intron_variant		1		ENSP00000402933.1

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47993 AN: 151736 Hom.: 9203 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.316 AC: 47998 AN: 151854 Hom.: 9200 Cov.: 31 AF XY: 0.310 AC XY: 22969 AN XY: 74166

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.353

Alfa AF: 0.410 Hom.: 27708

Bravo AF: 0.310

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.83
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7651825; hg19: chr3-14812118; COSMIC: COSV53786001; COSMIC: COSV53786001;