chr17-72598490-G-A

Variant names:

• chr17-72598490-G-A
• rs11077614
• ENST00000581549.2:n.1816C>T

Variant summary

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

The ENST00000581549.2(LINC00511):​n.1816C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,650 control chromosomes in the GnomAD database, including 14,946 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 0.42 (14946 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: LINC00511 ENST00000581549.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00511	NR_033876.1	n.1816C>T		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00511	ENST00000581549.2	n.1816C>T		non_coding_transcript_exon_variant	Exon 5 of 5	2
LINC00511	ENST00000647871.2	n.1539C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00511	ENST00000649074.1	n.1456C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64272 AN: 151556 Hom.: 14938 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.410

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.424 AC: 64297 AN: 151650 Hom.: 14946 Cov.: 31 AF XY: 0.424 AC XY: 31430 AN XY: 74052

African (AFR) AF: 0.265 AC: 10967 AN: 41310

American (AMR) AF: 0.388 AC: 5916 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1068 AN: 5172

South Asian (SAS) AF: 0.287 AC: 1377 AN: 4798

European-Finnish (FIN) AF: 0.596 AC: 6221 AN: 10440

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.531 AC: 36075 AN: 67904

Other (OTH) AF: 0.410 AC: 863 AN: 2104

Alfa AF: 0.484 Hom.: 49654

Bravo AF: 0.403

Asia WGS AF: 0.269 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs11077614; hg19: chr17-70594629;