ENST00000660463.1:n.889G>A

Variant names:

• chr20-1029145-C-T
• rs879012
• ENST00000660463.1:n.889G>A

Variant summary

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

The ENST00000660463.1(ENSG00000286787):​n.889G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,018 control chromosomes in the GnomAD database, including 32,825 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 0.65 (32825 hom., cov: 31)
• Consequence: ENSG00000286787 ENST00000660463.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950
• Publications: 3 publications found

Genes affected

ENSG00000286787 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.693 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
ENSG00000286787	ENST00000660463.1	n.889G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000286787	ENST00000664648.2	n.352+2239G>A		intron_variant	Intron 3 of 3
ENSG00000301438	ENST00000778881.1	n.216+16741C>T		intron_variant	Intron 2 of 3
ENSG00000301438	ENST00000778882.1	n.218+16741C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99456 AN: 151900 Hom.: 32814 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.655 AC: 99510 AN: 152018 Hom.: 32825 Cov.: 31 AF XY: 0.656 AC XY: 48731 AN XY: 74312

African (AFR) AF: 0.571 AC: 23653 AN: 41428

American (AMR) AF: 0.704 AC: 10759 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2477 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3058 AN: 5162

South Asian (SAS) AF: 0.668 AC: 3221 AN: 4820

European-Finnish (FIN) AF: 0.678 AC: 7165 AN: 10572

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47130 AN: 67970

Other (OTH) AF: 0.679 AC: 1433 AN: 2112

Alfa AF: 0.686 Hom.: 8699

Bravo AF: 0.652

Asia WGS AF: 0.630 AC: 2194 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.46
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs879012; hg19: chr20-1009788;