rs3130783

Positions:

• chr6-30806580-G-A
• chr6-30806580-G-T

Variant summary

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

The variant allele was found at a frequency of 0.75 in 151,084 control chromosomes in the GnomAD database, including 43,119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.75 (43119 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -0.630

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30806580G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000419357.6	n.146-7808C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113179 AN: 150968 Hom.: 43086 Cov.: 28

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.750 AC: 113267 AN: 151084 Hom.: 43119 Cov.: 28 AF XY: 0.755 AC XY: 55702 AN XY: 73756

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.738

Alfa AF: 0.747 Hom.: 6527

Bravo AF: 0.733

Asia WGS AF: 0.865 AC: 3008 AN: 3476

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130783; hg19: chr6-30774357;