chr18-42608028-A-T

Variant names:

• chr18-42608028-A-T
• rs10502793
• ENST00000589068.5:n.1236+32837A>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+32837A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,128 control chromosomes in the GnomAD database, including 1,594 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 0.10 (1594 hom., cov: 32)
• Consequence: LINC00907 ENST00000589068.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.1271+32837A>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+32837A>T		intron_variant	Intron 7 of 9	2
LINC00907	ENST00000753323.1	n.557-34891A>T		intron_variant	Intron 5 of 5
LINC00907	ENST00000753324.1	n.991+32837A>T		intron_variant	Intron 6 of 7
LINC00907	ENST00000753335.1	n.450+32837A>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15777 AN: 152010 Hom.: 1583 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0308

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.104 AC: 15821 AN: 152128 Hom.: 1594 Cov.: 32 AF XY: 0.106 AC XY: 7918 AN XY: 74380

African (AFR) AF: 0.223 AC: 9267 AN: 41480

American (AMR) AF: 0.0827 AC: 1264 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1910 AN: 5154

South Asian (SAS) AF: 0.111 AC: 535 AN: 4820

European-Finnish (FIN) AF: 0.0308 AC: 326 AN: 10600

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0307 AC: 2085 AN: 67996

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.00458 Hom.: 3

Bravo AF: 0.116

Asia WGS AF: 0.259 AC: 898 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.57
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs10502793; hg19: chr18-40187993;