rs1415130

chr13-23179740-C-T

Variant summary

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

The NM_001378244.1(SGCG):c.54+19094C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,958 control chromosomes in the GnomAD database, including 4,091 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 (4091 hom., cov: 32)
• Consequence: SGCG NM_001378244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19

Genes affected

SGCG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCG	NM_001378244.1	c.54+19094C>T		intron_variant
SGCG	XM_047430542.1	c.54+19094C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32298 AN: 151840 Hom.: 4091 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.213 AC: 32304 AN: 151958 Hom.: 4091 Cov.: 32 AF XY: 0.214 AC XY: 15885 AN XY: 74238

Gnomad4 AFR AF: 0.0787

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.218

Alfa AF: 0.229 Hom.: 952

Bravo AF: 0.202

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
Cadd	Benign	18
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1415130; hg19: chr13-23753879; COSMIC: COSV54562984;