rs759563

Variant names:

• chr17-72374747-C-T
• rs759563
• ENST00000581801.7:n.658-51427G>A

Variant summary

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

The ENST00000581801.7(LINC00511):​n.658-51427G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,972 control chromosomes in the GnomAD database, including 24,617 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 0.55 (24617 hom., cov: 32)
• Consequence: LINC00511 ENST00000581801.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 4 publications found

Genes affected

LINC00511 (HGNC:43564): (long intergenic non-protein coding RNA 511)

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 (AFR) allele frequency at 95% confidence interval = 0.729 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
LINC00511	ENST00000581801.7	n.658-51427G>A		intron_variant	Intron 2 of 2	3
LINC00511	ENST00000648088.1	n.491-51427G>A		intron_variant	Intron 1 of 1
LINC00511	ENST00000648248.1	n.394+53489G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84169 AN: 151854 Hom.: 24577 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.554 AC: 84267 AN: 151972 Hom.: 24617 Cov.: 32 AF XY: 0.550 AC XY: 40885 AN XY: 74280

African (AFR) AF: 0.736 AC: 30492 AN: 41436

American (AMR) AF: 0.602 AC: 9191 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1996 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1554 AN: 5152

South Asian (SAS) AF: 0.444 AC: 2137 AN: 4808

European-Finnish (FIN) AF: 0.408 AC: 4315 AN: 10572

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.480 AC: 32604 AN: 67948

Other (OTH) AF: 0.568 AC: 1197 AN: 2108

Alfa AF: 0.504 Hom.: 12013

Bravo AF: 0.577

Asia WGS AF: 0.412 AC: 1432 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	0.13
DANN	Benign	0.77
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs759563; hg19: chr17-70370888;