7-116508316-T-G

Variant names:

• chr7-116508316-T-G
• rs1052990
• NM_001233.5:c.*2195T>G

Variant summary

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

The NM_001233.5(CAV2):​c.*2195T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,820 control chromosomes in the GnomAD database, including 9,322 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 0.35 (9322 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: CAV2 NM_001233.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408

Genes affected

CAV2 (HGNC:1528): (caveolin 2) The protein encoded by this gene is a major component of the inner surface of caveolae, small invaginations of the plasma membrane, and is involved in essential cellular functions, including signal transduction, lipid metabolism, cellular growth control and apoptosis. This protein may function as a tumor suppressor. This gene and related family member (CAV1) are located next to each other on chromosome 7, and express colocalizing proteins that form a stable hetero-oligomeric complex. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. Additional isoforms resulting from the use of alternate in-frame translation initiation codons have also been described, and shown to have preferential localization in the cell (PMID:11238462). [provided by RefSeq, May 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAV2	NM_001233.5	c.*2195T>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000222693.5	NP_001224.1
CAV2	NM_001206747.2	c.*2195T>G		3_prime_UTR_variant	Exon 3 of 3		NP_001193676.1
CAV2	NM_198212.3	c.*2157T>G		3_prime_UTR_variant	Exon 2 of 2		NP_937855.1
CAV2	NM_001206748.2	c.*2195T>G		3_prime_UTR_variant	Exon 2 of 2		NP_001193677.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAV2	ENST00000222693.5	c.*2195T>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_001233.5	ENSP00000222693.4

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52456 AN: 151702 Hom.: 9319 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.347

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.346 AC: 52484 AN: 151820 Hom.: 9322 Cov.: 33 AF XY: 0.341 AC XY: 25310 AN XY: 74186

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.342

Alfa AF: 0.341 Hom.: 12383

Bravo AF: 0.350

Asia WGS AF: 0.206 AC: 720 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1052990; hg19: chr7-116148370;