rs6089784

Variant names:

• chr20-62768210-C-T
• rs6089784
• ENST00000770318.1:n.49+30C>T

Variant summary

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

The ENST00000770318.1(ENSG00000300239):​n.49+30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,020 control chromosomes in the GnomAD database, including 6,937 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 0.26 (6937 hom., cov: 32)
• Consequence: ENSG00000300239 ENST00000770318.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 7 publications found

Genes affected

ENSG00000300239 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 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
ENSG00000300239	ENST00000770318.1	n.49+30C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39883 AN: 151902 Hom.: 6924 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.263 AC: 39931 AN: 152020 Hom.: 6937 Cov.: 32 AF XY: 0.255 AC XY: 18957 AN XY: 74348

African (AFR) AF: 0.498 AC: 20623 AN: 41404

American (AMR) AF: 0.213 AC: 3263 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1235 AN: 5156

South Asian (SAS) AF: 0.162 AC: 782 AN: 4820

European-Finnish (FIN) AF: 0.0833 AC: 883 AN: 10600

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11506 AN: 67972

Other (OTH) AF: 0.268 AC: 563 AN: 2104

Alfa AF: 0.205 Hom.: 13293

Bravo AF: 0.283

Asia WGS AF: 0.201 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.3
DANN	Benign	0.67
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs6089784; hg19: chr20-61399562;