rs2569029

chr5-155813500-G-T

Variant summary

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

The XM_017009724.2(SGCD):c.-208+84510G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,002 control chromosomes in the GnomAD database, including 5,909 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 0.26 (5909 hom., cov: 32)
• Consequence: SGCD XM_017009724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

Genes affected

SGCD (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCD	XM_017009724.2	c.-208+84510G>T		intron_variant
SGCD	XM_047417518.1	c.-344-56844G>T		intron_variant
SGCD	XM_047417519.1	c.-288-56844G>T		intron_variant
SGCD	XM_047417520.1	c.-165+84510G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40029 AN: 151884 Hom.: 5904 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.263 AC: 40052 AN: 152002 Hom.: 5909 Cov.: 32 AF XY: 0.265 AC XY: 19707 AN XY: 74286

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.282

Alfa AF: 0.276 Hom.: 995

Bravo AF: 0.277

Asia WGS AF: 0.198 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	13
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2569029; hg19: chr5-155240510;