ENST00000634837.1:n.261+10711G>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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634837.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGO1-AS1	ENST00000634837.1	TSL:5	n.261+10711G>C		intron	N/A
	SGO1-AS1	ENST00000826894.1		n.73+10711G>C		intron	N/A
	SGO1-AS1	ENST00000826895.1		n.73+10711G>C		intron	N/A

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 v4.9

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;