2-191934410-A-G

Variant summary

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

The ENST00000424116.7(CAVIN2-AS1):n.238+87639A>G 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 0.258 in 152,066 control chromosomes in the GnomAD database, including 5,408 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 0.26 (5408 hom., cov: 32)
• Consequence: CAVIN2-AS1 ENST00000424116.7 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

Genes affected

CAVIN2-AS1 (HGNC:40517): (CAVIN2 and TMEFF2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAVIN2-AS1	ENST00000424116.7	n.238+87639A>G		intron_variant, non_coding_transcript_variant		2
CAVIN2-AS1	ENST00000428980.6	n.499+11366A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39158 AN: 151948 Hom.: 5384 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0844

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.258 AC: 39224 AN: 152066 Hom.: 5408 Cov.: 32 AF XY: 0.256 AC XY: 19050 AN XY: 74342

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.0848

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.238

Alfa AF: 0.210 Hom.: 1006

Bravo AF: 0.270

Asia WGS AF: 0.184 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.83
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4077949; hg19: chr2-192799136;