17-72367254-G-A

Position:

• chr17-72367254-G-A

Variant summary

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

The ENST00000648631.1(LINC00511):​n.1470+15789C>T 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 0.125 in 152,216 control chromosomes in the GnomAD database, including 1,372 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 0.12 (1372 hom., cov: 32)
• Consequence: LINC00511 ENST00000648631.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00511	ENST00000648631.1	n.1470+15789C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18989 AN: 152098 Hom.: 1371 Cov.: 32

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.125 AC: 18998 AN: 152216 Hom.: 1372 Cov.: 32 AF XY: 0.126 AC XY: 9345 AN XY: 74402

Gnomad4 AFR AF: 0.0807

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0180

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.136

Alfa AF: 0.136 Hom.: 2859

Bravo AF: 0.130

Asia WGS AF: 0.0770 AC: 269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12941150; hg19: chr17-70363395;