5-75998585-C-T

Position:

• chr5-75998585-C-T

Variant summary

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

The XM_011543282.4(SV2C):​c.-101-133065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,108 control chromosomes in the GnomAD database, including 51,647 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 0.82 (51647 hom., cov: 31)
• Consequence: SV2C XM_011543282.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

Genes affected

SV2C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SV2C	XM_011543282.4	c.-101-133065C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124944 AN: 151990 Hom.: 51593 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.822 AC: 125049 AN: 152108 Hom.: 51647 Cov.: 31 AF XY: 0.819 AC XY: 60870 AN XY: 74350

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.847

Alfa AF: 0.798 Hom.: 80726

Bravo AF: 0.827

Asia WGS AF: 0.749 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10214163; hg19: chr5-75294410;