chr5-5047765-C-T

Variant names:

• chr5-5047765-C-T
• rs272186
• ENST00000508201.5:n.309-3443C>T

Variant summary

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

The ENST00000508201.5(LINC01020):​n.309-3443C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 151,938 control chromosomes in the GnomAD database, including 45,084 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 0.77 (45084 hom., cov: 33)
• Consequence: LINC01020 ENST00000508201.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 1 publications found

Genes affected

LINC01020 (HGNC:27968): (long intergenic non-protein coding RNA 1020)

ENSG00000251426 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01020	NR_026994.1	n.308+8967C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01020	ENST00000508201.5	n.309-3443C>T		intron_variant	Intron 2 of 7	1
LINC01020	ENST00000509382.5	n.204+8967C>T		intron_variant	Intron 2 of 3	1
LINC01020	ENST00000507599.2	n.285-3413C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116247 AN: 151820 Hom.: 45045 Cov.: 33

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.766 AC: 116339 AN: 151938 Hom.: 45084 Cov.: 33 AF XY: 0.760 AC XY: 56411 AN XY: 74242

African (AFR) AF: 0.853 AC: 35339 AN: 41448

American (AMR) AF: 0.718 AC: 10963 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2772 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2578 AN: 5154

South Asian (SAS) AF: 0.625 AC: 3012 AN: 4822

European-Finnish (FIN) AF: 0.733 AC: 7724 AN: 10536

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.757 AC: 51417 AN: 67924

Other (OTH) AF: 0.750 AC: 1574 AN: 2100

Alfa AF: 0.770 Hom.: 12284

Bravo AF: 0.768

Asia WGS AF: 0.577 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.77
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs272186; hg19: chr5-5047878;