18-42608356-C-T

Variant names:

• chr18-42608356-C-T
• rs643272
• ENST00000589068.5:n.1236+33165C>T

Variant summary

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

The ENST00000589068.5(LINC00907):​n.1236+33165C>T variant causes a intron 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 ENST00000589068.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 3 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=-0.96).
• 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 rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.1271+33165C>T		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000589068.5	n.1236+33165C>T		intron_variant	Intron 7 of 9	2
LINC00907	ENST00000753323.1	n.557-34563C>T		intron_variant	Intron 5 of 5
LINC00907	ENST00000753324.1	n.991+33165C>T		intron_variant	Intron 6 of 7
LINC00907	ENST00000753335.1	n.450+33165C>T		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.806 AC: 31694 AN: 39322

American (AMR) AF: 0.406 AC: 5915 AN: 14558

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 860 AN: 3374

East Asian (EAS) AF: 0.735 AC: 3604 AN: 4902

South Asian (SAS) AF: 0.286 AC: 1302 AN: 4560

European-Finnish (FIN) AF: 0.278 AC: 2749 AN: 9888

Middle Eastern (MID) AF: 0.247 AC: 71 AN: 288

European-Non Finnish (NFE) AF: 0.268 AC: 17753 AN: 66222

Other (OTH) AF: 0.398 AC: 796 AN: 1998

Alfa AF: 0.382 Hom.: 1926

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs643272; hg19: chr18-40188321;