2-191934410-A-G

Variant names:

• chr2-191934410-A-G
• rs4077949
• ENST00000424116.8:n.241+87639A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000424116.8(CAVIN2-AS1):​n.241+87639A>G variant causes a intron 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 ENST00000424116.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CAVIN2-AS1	NR_187184.1	n.284+87639A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAVIN2-AS1	ENST00000424116.8	n.241+87639A>G		intron_variant	Intron 1 of 2	2
CAVIN2-AS1	ENST00000428980.6	n.499+11366A>G		intron_variant	Intron 1 of 4	5
CAVIN2-AS1	ENST00000792812.1	n.178+87639A>G		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.359 AC: 14871 AN: 41436

American (AMR) AF: 0.256 AC: 3909 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3472

East Asian (EAS) AF: 0.0848 AC: 439 AN: 5178

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4816

European-Finnish (FIN) AF: 0.165 AC: 1745 AN: 10578

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.230 AC: 15652 AN: 67988

Other (OTH) AF: 0.238 AC: 502 AN: 2112

Alfa AF: 0.222 Hom.: 1775

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
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs4077949; hg19: chr2-192799136;