20-5447654-C-T

Variant names:

• chr20-5447654-C-T
• rs10485489
• ENST00000593667.2:n.318-13253G>A

Variant summary

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

The ENST00000651499.1(ENSG00000230563):​n.427+1390C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 152,158 control chromosomes in the GnomAD database, including 183 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 0.041 (183 hom., cov: 33)
• Consequence: ENSG00000230563 ENST00000651499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 0 publications found

Genes affected

LINC00658 (HGNC:44315): (long intergenic non-protein coding RNA 658)

ENSG00000230563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651499.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00658	ENST00000593667.2	TSL:6	n.318-13253G>A		intron	N/A
	LINC00658	ENST00000600157.6	TSL:5	n.342+1010G>A		intron	N/A
	ENSG00000230563	ENST00000651499.1		n.427+1390C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6294 AN: 152040 Hom.: 185 Cov.: 33

Gnomad AFR AF: 0.0262

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0524

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0414 AC: 6296 AN: 152158 Hom.: 183 Cov.: 33 AF XY: 0.0438 AC XY: 3259 AN XY: 74384

African (AFR) AF: 0.0263 AC: 1092 AN: 41496

American (AMR) AF: 0.0524 AC: 802 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3470

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5184

South Asian (SAS) AF: 0.150 AC: 720 AN: 4816

European-Finnish (FIN) AF: 0.0440 AC: 466 AN: 10580

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0401 AC: 2730 AN: 67996

Other (OTH) AF: 0.0469 AC: 99 AN: 2110

Alfa AF: 0.0244 Hom.: 35

Bravo AF: 0.0380

Asia WGS AF: 0.0850 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.87
DANN	Benign	0.20
PhyloP100		-0.090
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10485489;

hg19: chr20-5428300;