13-23180605-T-G

Position:

• chr13-23180605-T-G

Variant summary

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

The NM_001378244.1(SGCG):​c.54+19959T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,118 control chromosomes in the GnomAD database, including 12,010 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 0.39 (12010 hom., cov: 33)
• Consequence: SGCG NM_001378244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

SGCG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCG	NM_001378244.1	c.54+19959T>G		intron_variant
SGCG	XM_047430542.1	c.54+19959T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58831 AN: 152000 Hom.: 11998 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.387 AC: 58882 AN: 152118 Hom.: 12010 Cov.: 33 AF XY: 0.384 AC XY: 28526 AN XY: 74352

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.387

Alfa AF: 0.448 Hom.: 26111

Bravo AF: 0.377

Asia WGS AF: 0.436 AC: 1515 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.31
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4770402; hg19: chr13-23754744;