chr18-42305834-G-A

Variant names:

• chr18-42305834-G-A
• rs10502782
• ENST00000585627.5:n.239+79727G>A

Variant summary

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

The ENST00000585627.5(LINC00907):​n.239+79727G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0753 in 151,946 control chromosomes in the GnomAD database, including 1,231 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 0.075 (1231 hom., cov: 32)
• Consequence: LINC00907 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.403-29250G>A		intron_variant	Intron 3 of 9
LINC00907	NR_046454.1	n.402+79727G>A		intron_variant	Intron 3 of 6
LINC00907	NR_046456.1	n.493+16240G>A		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.239+79727G>A		intron_variant	Intron 2 of 4	1
LINC00907	ENST00000585639.5	n.381+79727G>A		intron_variant	Intron 3 of 6	1
LINC00907	ENST00000586990.6	n.650-29250G>A		intron_variant	Intron 3 of 4	1

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11403 AN: 151828 Hom.: 1221 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00343

Gnomad OTH AF: 0.0634

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

GnomAD4 genome AF: 0.0753 AC: 11446 AN: 151946 Hom.: 1231 Cov.: 32 AF XY: 0.0776 AC XY: 5762 AN XY: 74272

African (AFR) AF: 0.171 AC: 7093 AN: 41404

American (AMR) AF: 0.0816 AC: 1245 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2268 AN: 5116

South Asian (SAS) AF: 0.0375 AC: 180 AN: 4800

European-Finnish (FIN) AF: 0.0234 AC: 248 AN: 10596

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00344 AC: 234 AN: 68000

Other (OTH) AF: 0.0694 AC: 146 AN: 2104

Alfa AF: 0.0243 Hom.: 506

Bravo AF: 0.0865

Asia WGS AF: 0.246 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10502782; hg19: chr18-39885799;