rs11699738

chr20-36861937-G-A

Variant summary

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

The NM_080627.4(SOGA1):c.687+721C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 152,316 control chromosomes in the GnomAD database, including 360 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 0.055 (360 hom., cov: 33)
• Consequence: SOGA1 NM_080627.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

Genes affected

SOGA1 (HGNC:16111): (microtubule crosslinking factor 2) Predicted to be involved in insulin receptor signaling pathway; negative regulation of gluconeogenesis; and regulation of autophagy. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.0944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOGA1	NM_080627.4	c.687+721C>T		intron_variant		ENST00000237536.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOGA1	ENST00000237536.9	c.687+721C>T		intron_variant		5	NM_080627.4	P2

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8442 AN: 152198 Hom.: 360 Cov.: 33

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.00952

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0554 AC: 8439 AN: 152316 Hom.: 360 Cov.: 33 AF XY: 0.0519 AC XY: 3864 AN XY: 74484

Gnomad4 AFR AF: 0.0158

Gnomad4 AMR AF: 0.0349

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.00953

Gnomad4 FIN AF: 0.0354

Gnomad4 NFE AF: 0.0963

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0808 Hom.: 765

Bravo AF: 0.0534

Asia WGS AF: 0.00606 AC: 22 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	5.7
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11699738; hg19: chr20-35490340;