18-42708328-C-T

Variant names:

• chr18-42708328-C-T
• rs8085804
• ENST00000753338.1:n.340-24153C>T

Variant summary

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

The ENST00000753338.1(LINC00907):​n.340-24153C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,942 control chromosomes in the GnomAD database, including 19,909 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 0.46 (19909 hom., cov: 32)
• Consequence: LINC00907 ENST00000753338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 11 publications found

Genes affected

LINC00907 (HGNC:44327): (long intergenic non-protein coding RNA 907)

ENSG00000286976 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 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
LINC00907	ENST00000753338.1	n.340-24153C>T		intron_variant	Intron 4 of 5
LINC00907	ENST00000753339.1	n.252-24153C>T		intron_variant	Intron 3 of 4
ENSG00000286976	ENST00000753521.1	n.70+33433G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70291 AN: 151822 Hom.: 19861 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.463 AC: 70404 AN: 151942 Hom.: 19909 Cov.: 32 AF XY: 0.466 AC XY: 34559 AN XY: 74240

African (AFR) AF: 0.770 AC: 31937 AN: 41484

American (AMR) AF: 0.512 AC: 7812 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 917 AN: 3466

East Asian (EAS) AF: 0.746 AC: 3823 AN: 5122

South Asian (SAS) AF: 0.410 AC: 1967 AN: 4802

European-Finnish (FIN) AF: 0.285 AC: 3013 AN: 10582

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19524 AN: 67928

Other (OTH) AF: 0.447 AC: 946 AN: 2116

Alfa AF: 0.351 Hom.: 38678

Bravo AF: 0.496

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs8085804; hg19: chr18-40288293;