3-20748689-T-C

Position:

• chr3-20748689-T-C

Variant summary

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

The ENST00000634618.1(SGO1-AS1):​n.1438+49244T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,886 control chromosomes in the GnomAD database, including 27,166 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 0.60 (27166 hom., cov: 32)
• Consequence: SGO1-AS1 ENST00000634618.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

Genes affected

SGO1-AS1 (HGNC:41081): (SGO1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGO1-AS1	ENST00000634618.1	n.1438+49244T>C		intron_variant, non_coding_transcript_variant		5
SGO1-AS1	ENST00000634837.1	n.117+16189T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90429 AN: 151768 Hom.: 27140 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.596 AC: 90504 AN: 151886 Hom.: 27166 Cov.: 32 AF XY: 0.600 AC XY: 44555 AN XY: 74228

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.575

Alfa AF: 0.584 Hom.: 39139

Bravo AF: 0.576

Asia WGS AF: 0.643 AC: 2232 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4857969; hg19: chr3-20790181;