ENST00000418663.5:n.605+26755C>T

Variant names:

• chr7-76578277-C-T
• rs17718068
• ENST00000418663.5:n.605+26755C>T

Variant summary

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

The ENST00000418663.5(LINC03009):​n.605+26755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,572 control chromosomes in the GnomAD database, including 5,255 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 0.25 (5255 hom., cov: 31)
• Consequence: LINC03009 ENST00000418663.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 1 publications found

Genes affected

LINC03009 (HGNC:56134): (long intergenic non-protein coding RNA 3009)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03009	NR_029411.1	n.624+26755C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03009	ENST00000418663.5	n.605+26755C>T		intron_variant	Intron 2 of 2	1
LINC03009	ENST00000450661.1	n.604+26755C>T		intron_variant	Intron 2 of 2	1
LINC03009	ENST00000423084.1	n.305+26755C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.251 AC: 37971 AN: 151454 Hom.: 5249 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0493

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.251 AC: 37978 AN: 151572 Hom.: 5255 Cov.: 31 AF XY: 0.245 AC XY: 18154 AN XY: 74058

African (AFR) AF: 0.177 AC: 7305 AN: 41368

American (AMR) AF: 0.219 AC: 3323 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1077 AN: 3450

East Asian (EAS) AF: 0.0496 AC: 256 AN: 5160

South Asian (SAS) AF: 0.230 AC: 1108 AN: 4818

European-Finnish (FIN) AF: 0.202 AC: 2124 AN: 10532

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21661 AN: 67766

Other (OTH) AF: 0.293 AC: 614 AN: 2096

Alfa AF: 0.166 Hom.: 336

Bravo AF: 0.250

Asia WGS AF: 0.116 AC: 404 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.93
DANN	Benign	0.77
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs17718068; hg19: chr7-76207594;