rs720201

Variant names:

• chr2-61149328-T-A
• rs720201
• ENST00000398622.3:n.-17+4132T>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000398622.3(C2orf74):​n.-17+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 ENST00000398622.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 26 publications found

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]

ENSG00000274769 (HGNC:):

C2orf74-AS1 (HGNC:56377): (C2orf74 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -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 rank	MANE	Protein	UniProt
C2orf74	NM_001143960.3	c.-122+4132T>A		intron_variant	Intron 1 of 3		NP_001137432.1
C2orf74	NM_001316317.2	c.-8+4132T>A		intron_variant	Intron 1 of 2		NP_001303246.1
C2orf74	NM_001367069.1	c.-273+4132T>A		intron_variant	Intron 1 of 4		NP_001353998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2orf74	ENST00000398622.3	n.-17+4132T>A		intron_variant	Intron 1 of 4	1		ENSP00000381621.2
C2orf74	ENST00000426997.5	c.-122+4132T>A		intron_variant	Intron 1 of 3	3		ENSP00000398725.1
C2orf74	ENST00000464909.2	c.-8+4132T>A		intron_variant	Intron 1 of 2	2		ENSP00000482798.1

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
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs720201; hg19: chr2-61376463;