20-23161018-T-C

Variant names:

• chr20-23161018-T-C
• rs844917
• ENST00000720384.1:n.162+1150T>C

Variant summary

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

The NR_199691.1(LINC03125):​n.409+1150T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,232 control chromosomes in the GnomAD database, including 53,262 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 0.84 (53219 hom., cov: 31)
  • Exomes 𝑓: 0.85 (43 hom.)
• Consequence: LINC03125 NR_199691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 3 publications found

Genes affected

LINC03125 (HGNC:57012):

RNA5SP478 (HGNC:43378): (RNA, 5S ribosomal pseudogene 478)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 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.409+1150T>C		intron	N/A
	LINC03125	NR_199692.1		n.409+1150T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03125	ENST00000720384.1		n.162+1150T>C		intron	N/A
	LINC03125	ENST00000720385.1		n.134+1150T>C		intron	N/A
	LINC03125	ENST00000720386.1		n.80+1150T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126933 AN: 151994 Hom.: 53169 Cov.: 31

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.855

GnomAD4 exome AF: 0.850 AC: 102 AN: 120 Hom.: 43 Cov.: 0 AF XY: 0.857 AC XY: 72 AN XY: 84

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 4 AN: 4

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AF: 1.00 AC: 4 AN: 4

European-Non Finnish (NFE) AF: 0.844 AC: 81 AN: 96

Other (OTH) AF: 0.875 AC: 7 AN: 8

GnomAD4 genome AF: 0.835 AC: 127043 AN: 152112 Hom.: 53219 Cov.: 31 AF XY: 0.833 AC XY: 61952 AN XY: 74346

African (AFR) AF: 0.856 AC: 35502 AN: 41494

American (AMR) AF: 0.832 AC: 12724 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2972 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4975 AN: 5176

South Asian (SAS) AF: 0.887 AC: 4273 AN: 4816

European-Finnish (FIN) AF: 0.720 AC: 7600 AN: 10558

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56185 AN: 67994

Other (OTH) AF: 0.857 AC: 1808 AN: 2110

Alfa AF: 0.836 Hom.: 111759

Bravo AF: 0.844

Asia WGS AF: 0.930 AC: 3232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.63
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs844917; hg19: chr20-23141655;