chr20-23151420-C-T

Variant names:

• chr20-23151420-C-T
• rs844906
• ENST00000778636.1:n.165-1124C>T

Variant summary

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

The NR_199691.1(LINC03125):​n.312+3006C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,964 control chromosomes in the GnomAD database, including 17,699 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 0.48 (17699 hom., cov: 32)
• Consequence: LINC03125 NR_199691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34
• Publications: 6 publications found

Genes affected

ENSG00000301398 (HGNC:):

LINC03125 (HGNC:57012):

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 = 0.549 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_199691.1. 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
	LINC03125	NR_199691.1		n.312+3006C>T		intron	N/A
	LINC03125	NR_199692.1		n.312+3006C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301398	ENST00000778636.1		n.165-1124C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72423 AN: 151844 Hom.: 17679 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.477 AC: 72470 AN: 151964 Hom.: 17699 Cov.: 32 AF XY: 0.475 AC XY: 35258 AN XY: 74278

African (AFR) AF: 0.370 AC: 15333 AN: 41446

American (AMR) AF: 0.559 AC: 8537 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1795 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2500 AN: 5134

South Asian (SAS) AF: 0.519 AC: 2502 AN: 4820

European-Finnish (FIN) AF: 0.437 AC: 4618 AN: 10566

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35287 AN: 67934

Other (OTH) AF: 0.520 AC: 1096 AN: 2106

Alfa AF: 0.492 Hom.: 3098

Bravo AF: 0.482

Asia WGS AF: 0.517 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.59
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs844906; hg19: chr20-23132057;