18-42181378-C-T

Variant names:

• chr18-42181378-C-T
• rs10502778
• ENST00000601948.5:n.196-4789C>T

Variant summary

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

The ENST00000601948.5(LINC00907):​n.196-4789C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0887 in 152,128 control chromosomes in the GnomAD database, including 1,437 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 0.089 (1437 hom., cov: 32)
• Consequence: LINC00907 ENST00000601948.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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	ENST00000601948.5	n.196-4789C>T		intron_variant	Intron 1 of 4	5
LINC00907	ENST00000659948.1	n.79+21901C>T		intron_variant	Intron 1 of 3
LINC00907	ENST00000753323.1	n.71+21901C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0887 AC: 13477 AN: 152010 Hom.: 1431 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00806

Gnomad OTH AF: 0.0653

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

GnomAD4 genome AF: 0.0887 AC: 13494 AN: 152128 Hom.: 1437 Cov.: 32 AF XY: 0.0907 AC XY: 6746 AN XY: 74354

African (AFR) AF: 0.215 AC: 8942 AN: 41506

American (AMR) AF: 0.0694 AC: 1060 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00952 AC: 33 AN: 3468

East Asian (EAS) AF: 0.366 AC: 1889 AN: 5158

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4824

European-Finnish (FIN) AF: 0.0511 AC: 541 AN: 10588

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00807 AC: 549 AN: 67992

Other (OTH) AF: 0.0703 AC: 148 AN: 2104

Alfa AF: 0.0255 Hom.: 131

Bravo AF: 0.0990

Asia WGS AF: 0.203 AC: 704 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs10502778; hg19: chr18-39761342;