20-23169102-A-G

Variant names:

• chr20-23169102-A-G
• rs10485640
• ENST00000720384.1:n.162+9234A>G

Variant summary

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

The ENST00000720384.1(LINC03125):​n.162+9234A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 152,296 control chromosomes in the GnomAD database, including 546 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 0.070 (546 hom., cov: 33)
• Consequence: LINC03125 ENST00000720384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.875
• Publications: 4 publications found

Genes affected

LINC03125 (HGNC:57012):

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 (NFE) allele frequency at 95% confidence interval = 0.0965 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720384.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03125	NR_199691.1		n.409+9234A>G		intron	N/A
	LINC03125	NR_199692.1		n.409+9234A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03125	ENST00000720384.1		n.162+9234A>G		intron	N/A
	LINC03125	ENST00000720385.1		n.134+9234A>G		intron	N/A
	LINC03125	ENST00000720386.1		n.80+9234A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0699 AC: 10633 AN: 152178 Hom.: 547 Cov.: 33

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0652

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0698 AC: 10629 AN: 152296 Hom.: 546 Cov.: 33 AF XY: 0.0723 AC XY: 5385 AN XY: 74466

African (AFR) AF: 0.0163 AC: 678 AN: 41570

American (AMR) AF: 0.0651 AC: 996 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0472 AC: 228 AN: 4828

European-Finnish (FIN) AF: 0.154 AC: 1630 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0985 AC: 6699 AN: 68018

Other (OTH) AF: 0.0610 AC: 129 AN: 2114

Alfa AF: 0.0794 Hom.: 448

Bravo AF: 0.0610

Asia WGS AF: 0.0170 AC: 58 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	3.3
DANN	Benign	0.31
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs10485640; hg19: chr20-23149739;