rs10512584

chr17-72296621-A-Cchr17-72296621-A-T

Variant summary

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

The ENST00000648631.1(LINC00511):n.1471-5072T>G 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 0.212 in 152,248 control chromosomes in the GnomAD database, including 3,670 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 0.21 (3670 hom., cov: 33)
• Consequence: LINC00511 ENST00000648631.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 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.1471-5072T>G		intron_variant, non_coding_transcript_variant
LINC00511	ENST00000648248.1	n.395-5072T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32205 AN: 152130 Hom.: 3666 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.212 AC: 32233 AN: 152248 Hom.: 3670 Cov.: 33 AF XY: 0.213 AC XY: 15871 AN XY: 74436

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.215

Alfa AF: 0.222 Hom.: 7540

Bravo AF: 0.212

Asia WGS AF: 0.306 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	13
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512584; hg19: chr17-70292762;