3-20916318-G-C

Variant names:

• chr3-20916318-G-C
• rs6787231
• ENST00000634837.1:n.261+10711G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634837.1(SGO1-AS1):​n.261+10711G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,322 control chromosomes in the GnomAD database, including 68,800 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 0.95 (68800 hom., cov: 33)
• Consequence: SGO1-AS1 ENST00000634837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 4 publications found

Genes affected

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

LOC107986068 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986068	XR_001740619.2	n.88+10711G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGO1-AS1	ENST00000634837.1	n.261+10711G>C		intron_variant	Intron 3 of 7	5
SGO1-AS1	ENST00000826894.1	n.73+10711G>C		intron_variant	Intron 1 of 5
SGO1-AS1	ENST00000826895.1	n.73+10711G>C		intron_variant	Intron 1 of 5
SGO1-AS1	ENST00000826896.1	n.96+10711G>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144604 AN: 152204 Hom.: 68741 Cov.: 33

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.950 AC: 144722 AN: 152322 Hom.: 68800 Cov.: 33 AF XY: 0.952 AC XY: 70905 AN XY: 74484

African (AFR) AF: 0.987 AC: 41040 AN: 41584

American (AMR) AF: 0.964 AC: 14742 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3322 AN: 3472

East Asian (EAS) AF: 0.956 AC: 4949 AN: 5178

South Asian (SAS) AF: 0.945 AC: 4563 AN: 4828

European-Finnish (FIN) AF: 0.960 AC: 10193 AN: 10622

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62880 AN: 68030

Other (OTH) AF: 0.965 AC: 2041 AN: 2116

Alfa AF: 0.921 Hom.: 3011

Bravo AF: 0.951

Asia WGS AF: 0.956 AC: 3325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.23
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6787231; hg19: chr3-20957810;