17-72296621-A-C

Variant names:

• chr17-72296621-A-C
• rs10512584
• ENST00000648248.1:n.395-5072T>G

Variant summary

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

The ENST00000648248.1(LINC00511):​n.395-5072T>G variant causes a intron 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 ENST00000648248.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00511	ENST00000648248.1	n.395-5072T>G		intron_variant	Intron 3 of 3
LINC00511	ENST00000648631.1	n.1471-5072T>G		intron_variant	Intron 5 of 5

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;