20-6355950-G-A

Variant names:

• chr20-6355950-G-A
• rs3920632
• ENST00000823994.1:n.*105G>A

Variant summary

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

The ENST00000823994.1(ENSG00000307125):​n.*105G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,128 control chromosomes in the GnomAD database, including 8,132 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 0.30 (8132 hom., cov: 33)
• Consequence: ENSG00000307125 ENST00000823994.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 2 publications found

Genes affected

ENSG00000307125 (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 (EAS) allele frequency at 95% confidence interval = 0.75 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
ENSG00000307125	ENST00000823994.1	n.*105G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45376 AN: 152008 Hom.: 8126 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.298 AC: 45393 AN: 152128 Hom.: 8132 Cov.: 33 AF XY: 0.309 AC XY: 22954 AN XY: 74354

African (AFR) AF: 0.151 AC: 6291 AN: 41530

American (AMR) AF: 0.413 AC: 6317 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1174 AN: 3472

East Asian (EAS) AF: 0.770 AC: 3978 AN: 5168

South Asian (SAS) AF: 0.401 AC: 1929 AN: 4812

European-Finnish (FIN) AF: 0.404 AC: 4265 AN: 10552

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20402 AN: 67986

Other (OTH) AF: 0.329 AC: 695 AN: 2112

Alfa AF: 0.306 Hom.: 10777

Bravo AF: 0.301

Asia WGS AF: 0.522 AC: 1815 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	6.0
DANN	Benign	0.48
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs3920632; hg19: chr20-6336597;