chr5-5047765-C-T

Position:

• chr5-5047765-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01020 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01020	NR_026994.1	n.308+8967C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01020	ENST00000508201.5	n.309-3443C>T		intron_variant		1
LINC01020	ENST00000509382.5	n.204+8967C>T		intron_variant		1
LINC01020	ENST00000507599.2	n.285-3413C>T		intron_variant		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

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.750

Alfa AF: 0.768 Hom.: 10844

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs272186; hg19: chr5-5047878;