rs6082986

Variant names:

• chr20-23043282-A-G
• rs6082986
• ENST00000739851.1:n.796-1531T>C

Variant summary

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

The ENST00000739851.1(ENSG00000296483):​n.796-1531T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,180 control chromosomes in the GnomAD database, including 8,861 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 0.34 (8861 hom., cov: 33)
• Consequence: ENSG00000296483 ENST00000739851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 10 publications found

Genes affected

ENSG00000296483 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296483	ENST00000739851.1	n.796-1531T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51212 AN: 152062 Hom.: 8867 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.337 AC: 51225 AN: 152180 Hom.: 8861 Cov.: 33 AF XY: 0.339 AC XY: 25242 AN XY: 74406

African (AFR) AF: 0.260 AC: 10820 AN: 41538

American (AMR) AF: 0.319 AC: 4873 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1270 AN: 5180

South Asian (SAS) AF: 0.471 AC: 2264 AN: 4810

European-Finnish (FIN) AF: 0.326 AC: 3453 AN: 10596

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25632 AN: 67972

Other (OTH) AF: 0.354 AC: 748 AN: 2112

Alfa AF: 0.335 Hom.: 1691

Bravo AF: 0.327

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.53
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs6082986; hg19: chr20-23023919;