rs17138767

Positions:

• chr7-116497623-A-G

Variant summary

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

The ENST00000462876.5(CAV2):​n.1007-146A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,276 control chromosomes in the GnomAD database, including 610 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 0.072 (610 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: CAV2 ENST00000462876.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

CAV2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986838	NR_188009.1	n.163+1731T>C		intron_variant
LOC107986838	NR_188010.1	n.163+1731T>C		intron_variant
LOC107986838	NR_188011.1	n.163+1731T>C		intron_variant
LOC107986838	NR_188012.1	n.163+1731T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAV2	ENST00000462876.5	n.1007-146A>G		intron_variant		1
CAV2	ENST00000467035.5	n.753-146A>G		intron_variant		1
CAV2	ENST00000472470.5	n.407-146A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10985 AN: 152158 Hom.: 612 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.0544

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.0721 AC: 10982 AN: 152274 Hom.: 610 Cov.: 32 AF XY: 0.0774 AC XY: 5761 AN XY: 74448

Gnomad4 AFR AF: 0.0292

Gnomad4 AMR AF: 0.0827

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.0727

Gnomad4 OTH AF: 0.0534

Alfa AF: 0.0660 Hom.: 41

Bravo AF: 0.0649

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17138767; hg19: chr7-116137677;