rs759563

Positions:

• chr17-72374747-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648631.1(LINC00511):​n.1470+8296G>A variant causes a intron, non coding transcript 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 ENST00000648631.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00511	ENST00000648631.1	n.1470+8296G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.568

Alfa AF: 0.502 Hom.: 10803

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs759563; hg19: chr17-70370888;