rs720201

Positions:

• chr2-61149328-T-A
• chr2-61149328-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001143960.3(C2orf74):​c.-122+4132T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: C2orf74 NM_001143960.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

C2orf74 (HGNC:34439): (chromosome 2 open reading frame 74) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2orf74	NM_001143960.3	c.-122+4132T>A		intron_variant			NP_001137432.1
C2orf74	NM_001316317.2	c.-8+4132T>A		intron_variant			NP_001303246.1
C2orf74	NM_001367069.1	c.-273+4132T>A		intron_variant			NP_001353998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C2orf74	ENST00000398622.3	c.-17+4132T>A		intron_variant, NMD_transcript_variant		1		ENSP00000381621
C2orf74	ENST00000426997.5	c.-122+4132T>A		intron_variant		3		ENSP00000398725
C2orf74	ENST00000464909.2	c.-8+4132T>A		intron_variant		2		ENSP00000482798
C2orf74	ENST00000489686.5	c.-273+4132T>A		intron_variant		5		ENSP00000481253

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720201; hg19: chr2-61376463;