rs6776153

chr3-20916359-A-Gchr3-20916359-A-T

Variant summary

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

The XR_001740619.2(LOC107986068):n.88+10752A>G 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 0.519 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: LOC107986068 XR_001740619.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

Genes affected

LOC107986068 (HGNC:):

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=-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/exons	MANE	UniProt
LOC107986068	XR_001740619.2	n.88+10752A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGO1-AS1	ENST00000634837.1	n.261+10752A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.498

Alfa AF: 0.453 Hom.: 11981

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6776153; hg19: chr3-20957851;