rs10044666

chr5-155749010-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+20020G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,088 control chromosomes in the GnomAD database, including 4,549 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 0.24 (4549 hom., cov: 32)
• Consequence: SGCD XM_017009724.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

SGCD (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCD	XM_017009724.2	c.-208+20020G>T		intron_variant
SGCD	XM_047417518.1	c.-345+20020G>T		intron_variant
SGCD	XM_047417519.1	c.-289+20020G>T		intron_variant
SGCD	XM_047417520.1	c.-165+20020G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36385 AN: 151970 Hom.: 4546 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.239 AC: 36406 AN: 152088 Hom.: 4549 Cov.: 32 AF XY: 0.241 AC XY: 17901 AN XY: 74338

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.233

Alfa AF: 0.256 Hom.: 8363

Bravo AF: 0.230

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	0.71
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10044666; hg19: chr5-155128570; COSMIC: COSV60219189;