ENST00000581801.7:n.658-43934C>T

Variant names:

• chr17-72367254-G-A
• rs12941150
• ENST00000581801.7:n.658-43934C>T

Variant summary

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

The ENST00000581801.7(LINC00511):​n.658-43934C>T variant causes a intron 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 ENST00000581801.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 7 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=-0.85).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00511	ENST00000581801.7	n.658-43934C>T		intron_variant	Intron 2 of 2	3
LINC00511	ENST00000648088.1	n.491-43934C>T		intron_variant	Intron 1 of 1
LINC00511	ENST00000648248.1	n.394+60982C>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.0807 AC: 3354 AN: 41538

American (AMR) AF: 0.241 AC: 3682 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3468

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5180

South Asian (SAS) AF: 0.116 AC: 558 AN: 4822

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10590

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9299 AN: 68012

Other (OTH) AF: 0.136 AC: 288 AN: 2112

Alfa AF: 0.134 Hom.: 5245

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs12941150; hg19: chr17-70363395;