18-42608356-C-T

Position:

• chr18-42608356-C-T

Variant summary

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

The NR_046174.2(LINC00907):​n.1271+33165C>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 0.445 in 146,008 control chromosomes in the GnomAD database, including 19,017 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 0.44 (19017 hom., cov: 29)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00907	NR_046174.2	n.1271+33165C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000589068.5	n.1236+33165C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.444 AC: 64830 AN: 145896 Hom.: 18975 Cov.: 29

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.445 AC: 64929 AN: 146008 Hom.: 19017 Cov.: 29 AF XY: 0.444 AC XY: 31593 AN XY: 71106

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.398

Alfa AF: 0.364 Hom.: 1674

Bravo AF: 0.477

Asia WGS AF: 0.464 AC: 1412 AN: 3044

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs643272; hg19: chr18-40188321;