rs27065

Variant names:

• chr5-1359140-G-A
• rs27065
• ENST00000653645.1:n.437-3605C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-1359140-G-A
• chr5-1359140-G-C

Variant summary

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

The ENST00000653645.1(LINC01511):​n.437-3605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,924 control chromosomes in the GnomAD database, including 17,099 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 0.47 (17099 hom., cov: 32)
• Consequence: LINC01511 ENST00000653645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01511	ENST00000653645.1	n.437-3605C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71273 AN: 151806 Hom.: 17089 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.469 AC: 71320 AN: 151924 Hom.: 17099 Cov.: 32 AF XY: 0.471 AC XY: 34930 AN XY: 74236

African (AFR) AF: 0.367 AC: 15218 AN: 41452

American (AMR) AF: 0.516 AC: 7885 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2708 AN: 5128

South Asian (SAS) AF: 0.606 AC: 2918 AN: 4816

European-Finnish (FIN) AF: 0.473 AC: 4995 AN: 10570

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34604 AN: 67890

Other (OTH) AF: 0.455 AC: 962 AN: 2114

Alfa AF: 0.491 Hom.: 2352

Bravo AF: 0.468

Asia WGS AF: 0.540 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.86
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs27065; hg19: chr5-1359255;