rs6776153

Variant names:

• chr3-20916359-A-G
• rs6776153
• ENST00000634837.1:n.261+10752A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-20916359-A-G
• chr3-20916359-A-T

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+10752A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,074 control chromosomes in the GnomAD database, including 21,666 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 0.52 (21666 hom., cov: 32)
• Consequence: SGO1-AS1 ENST00000634837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986068	XR_001740619.2	n.88+10752A>G		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+10752A>G		intron_variant	Intron 3 of 7	5
SGO1-AS1	ENST00000826894.1	n.73+10752A>G		intron_variant	Intron 1 of 5
SGO1-AS1	ENST00000826895.1	n.73+10752A>G		intron_variant	Intron 1 of 5
SGO1-AS1	ENST00000826896.1	n.96+10752A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78838 AN: 151956 Hom.: 21628 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.519 AC: 78927 AN: 152074 Hom.: 21666 Cov.: 32 AF XY: 0.516 AC XY: 38329 AN XY: 74336

African (AFR) AF: 0.685 AC: 28396 AN: 41466

American (AMR) AF: 0.443 AC: 6759 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1705 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3355 AN: 5164

South Asian (SAS) AF: 0.679 AC: 3276 AN: 4822

European-Finnish (FIN) AF: 0.361 AC: 3820 AN: 10580

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30069 AN: 67990

Other (OTH) AF: 0.498 AC: 1049 AN: 2108

Alfa AF: 0.456 Hom.: 15085

Bravo AF: 0.528

Asia WGS AF: 0.607 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.99
DANN	Benign	0.74
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs6776153; hg19: chr3-20957851;