chr18-42443817-G-A

Variant names:

• chr18-42443817-G-A
• rs12606301
• ENST00000585627.5:n.240-10115G>A

Variant summary

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

The ENST00000585627.5(LINC00907):​n.240-10115G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 150,866 control chromosomes in the GnomAD database, including 2,060 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 0.14 (2060 hom., cov: 28)
• Consequence: LINC00907 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.623-10115G>A		intron_variant	Intron 4 of 9
LINC00907	NR_046454.1	n.403-10115G>A		intron_variant	Intron 3 of 6
LINC00907	NR_046456.1	n.714-10115G>A		intron_variant	Intron 5 of 7
LINC00907	NR_046457.1	n.494-10115G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.240-10115G>A		intron_variant	Intron 2 of 4	1
LINC00907	ENST00000585639.5	n.382-10115G>A		intron_variant	Intron 3 of 6	1
LINC00907	ENST00000591381.5	n.223-10115G>A		intron_variant	Intron 2 of 4	1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21449 AN: 150748 Hom.: 2054 Cov.: 28

Gnomad AFR AF: 0.0870

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.142 AC: 21468 AN: 150866 Hom.: 2060 Cov.: 28 AF XY: 0.144 AC XY: 10634 AN XY: 73594

African (AFR) AF: 0.0872 AC: 3581 AN: 41084

American (AMR) AF: 0.224 AC: 3370 AN: 15042

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3468

East Asian (EAS) AF: 0.527 AC: 2681 AN: 5086

South Asian (SAS) AF: 0.0950 AC: 448 AN: 4714

European-Finnish (FIN) AF: 0.112 AC: 1173 AN: 10436

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9173 AN: 67740

Other (OTH) AF: 0.163 AC: 340 AN: 2090

Alfa AF: 0.142 Hom.: 3275

Bravo AF: 0.153

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.17
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs12606301; hg19: chr18-40023782;