rs6028466

Variant names:

• chr20-39500359-G-A
• rs6028466
• ENST00000774323.1:n.209+31937G>A

Variant summary

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

The ENST00000774323.1(ENSG00000300834):​n.209+31937G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,186 control chromosomes in the GnomAD database, including 1,668 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 0.11 (1668 hom., cov: 33)
• Consequence: ENSG00000300834 ENST00000774323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.974
• Publications: 32 publications found

Genes affected

ENSG00000300834 (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 = 0.258 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
ENSG00000300834	ENST00000774323.1	n.209+31937G>A		intron_variant	Intron 2 of 2
ENSG00000300834	ENST00000774324.1	n.86-3358G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16688 AN: 152070 Hom.: 1655 Cov.: 33

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0692

Gnomad ASJ AF: 0.0711

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.110 AC: 16738 AN: 152186 Hom.: 1668 Cov.: 33 AF XY: 0.106 AC XY: 7883 AN XY: 74382

African (AFR) AF: 0.262 AC: 10853 AN: 41464

American (AMR) AF: 0.0691 AC: 1056 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0711 AC: 247 AN: 3472

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5180

South Asian (SAS) AF: 0.0379 AC: 183 AN: 4828

European-Finnish (FIN) AF: 0.0183 AC: 194 AN: 10612

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0561 AC: 3815 AN: 68022

Other (OTH) AF: 0.104 AC: 221 AN: 2116

Alfa AF: 0.0704 Hom.: 2135

Bravo AF: 0.120

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	0.49
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs6028466; hg19: chr20-38129002;