chr7-116497838-T-G

Position:

• chr7-116497838-T-G

Variant summary

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

The ENST00000462876.5(CAV2):​n.1076T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,232 control chromosomes in the GnomAD database, including 1,919 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 0.15 (1918 hom., cov: 33)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: CAV2 ENST00000462876.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

Genes affected

CAV2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986838	NR_188009.1	n.163+1516A>C		intron_variant
LOC107986838	NR_188010.1	n.163+1516A>C		intron_variant
LOC107986838	NR_188011.1	n.163+1516A>C		intron_variant
LOC107986838	NR_188012.1	n.163+1516A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAV2	ENST00000462876.5	n.1076T>G		non_coding_transcript_exon_variant	9/14	1
CAV2	ENST00000467035.5	n.822T>G		non_coding_transcript_exon_variant	7/9	1
CAV2	ENST00000472470.5	n.476T>G		non_coding_transcript_exon_variant	4/6	1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23252 AN: 152108 Hom.: 1919 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.174

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.153 AC: 23262 AN: 152226 Hom.: 1918 Cov.: 33 AF XY: 0.148 AC XY: 11044 AN XY: 74452

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.172

Alfa AF: 0.180 Hom.: 3473

Bravo AF: 0.158

Asia WGS AF: 0.0790 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.72
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4730742; hg19: chr7-116137892;