rs2167564

chr2-61173681-G-A

Variant summary

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

The NR_183879.1(C2orf74-AS1):n.180+4425C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,042 control chromosomes in the GnomAD database, including 14,736 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 0.43 (14736 hom., cov: 33)
• Consequence: C2orf74-AS1 NR_183879.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

C2orf74-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf74-AS1	NR_183879.1	n.180+4425C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.434 AC: 66010 AN: 151924 Hom.: 14708 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.435 AC: 66087 AN: 152042 Hom.: 14736 Cov.: 33 AF XY: 0.436 AC XY: 32371 AN XY: 74312

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.456

Alfa AF: 0.429 Hom.: 1753

Bravo AF: 0.430

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.2
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2167564; hg19: chr2-61400816;