5-155775518-A-G

Position:

• chr5-155775518-A-G

Variant summary

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

The XM_017009724.2(SGCD):​c.-208+46528A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 152,112 control chromosomes in the GnomAD database, including 325 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 0.045 (325 hom., cov: 32)
• Consequence: SGCD XM_017009724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

SGCD (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGCD	XM_017009724.2	c.-208+46528A>G		intron_variant			XP_016865213.1
SGCD	XM_047417518.1	c.-345+46528A>G		intron_variant			XP_047273474.1
SGCD	XM_047417519.1	c.-289+46528A>G		intron_variant			XP_047273475.1
SGCD	XM_047417520.1	c.-165+46528A>G		intron_variant			XP_047273476.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0445 AC: 6765 AN: 151994 Hom.: 324 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0446 AC: 6785 AN: 152112 Hom.: 325 Cov.: 32 AF XY: 0.0436 AC XY: 3244 AN XY: 74346

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0273

Gnomad4 ASJ AF: 0.0418

Gnomad4 EAS AF: 0.0466

Gnomad4 SAS AF: 0.0436

Gnomad4 FIN AF: 0.00349

Gnomad4 NFE AF: 0.0109

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0138 Hom.: 19

Bravo AF: 0.0510

Asia WGS AF: 0.0530 AC: 184 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11134474; hg19: chr5-155202528;