17-72588126-C-T

Position:

• chr17-72588126-C-T

Variant summary

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

The ENST00000453722.6(LINC00511):​n.602+4077G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,080 control chromosomes in the GnomAD database, including 41,335 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 0.72 (41335 hom., cov: 32)
• Consequence: LINC00511 ENST00000453722.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947

Genes affected

LINC00511 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00673	NR_036488.1	n.602+4077G>A		intron_variant
LINC00673	NR_137280.2	n.602+4077G>A		intron_variant
LINC00673	NR_137281.2	n.602+4077G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00511	ENST00000453722.6	n.602+4077G>A		intron_variant		2
LINC00511	ENST00000580861.2	n.407+14977G>A		intron_variant		4
LINC00511	ENST00000581801.7	n.594+4077G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109238 AN: 151962 Hom.: 41317 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.719 AC: 109302 AN: 152080 Hom.: 41335 Cov.: 32 AF XY: 0.718 AC XY: 53405 AN XY: 74368

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.729

Alfa AF: 0.814 Hom.: 100750

Bravo AF: 0.699

Asia WGS AF: 0.612 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718073; hg19: chr17-70584265;