rs12657643

Positions:

• chr5-75995992-A-G
• chr5-75995992-A-T

Variant summary

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

The XM_011543282.4(SV2C):​c.-101-135658A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,146 control chromosomes in the GnomAD database, including 3,924 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 0.21 (3924 hom., cov: 32)
• Consequence: SV2C XM_011543282.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

Genes affected

SV2C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SV2C	XM_011543282.4	c.-101-135658A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31342 AN: 152028 Hom.: 3913 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.206 AC: 31377 AN: 152146 Hom.: 3924 Cov.: 32 AF XY: 0.214 AC XY: 15887 AN XY: 74384

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.235

Alfa AF: 0.149 Hom.: 2588

Bravo AF: 0.219

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12657643; hg19: chr5-75291817;