18-42181378-C-T

Position:

• chr18-42181378-C-T

Variant summary

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

The ENST00000601948.5(LINC00907):​n.196-4789C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000601948.5	n.196-4789C>T		intron_variant, non_coding_transcript_variant		5
LINC00907	ENST00000659948.1	n.79+21901C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0694

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.0678

Gnomad4 FIN AF: 0.0511

Gnomad4 NFE AF: 0.00807

Gnomad4 OTH AF: 0.0703

Alfa AF: 0.0268 Hom.: 123

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502778; hg19: chr18-39761342;