18-42618612-T-G

Variant names:

• chr18-42618612-T-G
• rs2163385
• ENST00000589068.5:n.1236+43421T>G

Variant summary

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

The ENST00000589068.5(LINC00907):​n.1236+43421T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 152,192 control chromosomes in the GnomAD database, including 441 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 0.072 (441 hom., cov: 32)
• Consequence: LINC00907 ENST00000589068.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589068.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00907	NR_046174.2		n.1271+43421T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00907	ENST00000589068.5	TSL:2	n.1236+43421T>G		intron	N/A
	LINC00907	ENST00000753323.1		n.557-24307T>G		intron	N/A
	LINC00907	ENST00000753324.1		n.992-24307T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0721 AC: 10960 AN: 152074 Hom.: 441 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0326

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0595

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0720 AC: 10962 AN: 152192 Hom.: 441 Cov.: 32 AF XY: 0.0713 AC XY: 5308 AN XY: 74442

African (AFR) AF: 0.109 AC: 4530 AN: 41502

American (AMR) AF: 0.0477 AC: 728 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3472

East Asian (EAS) AF: 0.0942 AC: 487 AN: 5168

South Asian (SAS) AF: 0.105 AC: 504 AN: 4816

European-Finnish (FIN) AF: 0.0326 AC: 346 AN: 10616

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0595 AC: 4049 AN: 68020

Other (OTH) AF: 0.0705 AC: 149 AN: 2114

Alfa AF: 0.0571 Hom.: 493

Bravo AF: 0.0740

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.14
DANN	Benign	0.49
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2163385; hg19: chr18-40198577;