5-1362678-T-C

Variant names:

• chr5-1362678-T-C
• rs27061
• ENST00000653645.1:n.437-7143A>G

Variant summary

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

The ENST00000653645.1(LINC01511):​n.437-7143A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,030 control chromosomes in the GnomAD database, including 21,398 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 0.52 (21398 hom., cov: 33)
• Consequence: LINC01511 ENST00000653645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413
• Publications: 13 publications found

Genes affected

LINC01511 (HGNC:51200): (long intergenic non-protein coding RNA 1511)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653645.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01511	ENST00000653645.1		n.437-7143A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79590 AN: 151912 Hom.: 21388 Cov.: 33

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.524 AC: 79632 AN: 152030 Hom.: 21398 Cov.: 33 AF XY: 0.524 AC XY: 38951 AN XY: 74304

African (AFR) AF: 0.395 AC: 16370 AN: 41440

American (AMR) AF: 0.559 AC: 8539 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3466

East Asian (EAS) AF: 0.537 AC: 2775 AN: 5166

South Asian (SAS) AF: 0.645 AC: 3110 AN: 4824

European-Finnish (FIN) AF: 0.536 AC: 5652 AN: 10550

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39739 AN: 67988

Other (OTH) AF: 0.510 AC: 1076 AN: 2108

Alfa AF: 0.553 Hom.: 59852

Bravo AF: 0.519

Asia WGS AF: 0.566 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.23
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs27061; hg19: chr5-1362793;