18-42478917-T-C

Variant names:

• chr18-42478917-T-C
• rs7235528
• ENST00000585627.5:n.489+23928T>C

Variant summary

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

The ENST00000585627.5(LINC00907):​n.489+23928T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,162 control chromosomes in the GnomAD database, including 6,271 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 0.25 (6271 hom., cov: 33)
• Consequence: LINC00907 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896
• Publications: 9 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.872+23928T>C		intron_variant	Intron 6 of 9
LINC00907	NR_046454.1	n.652+23928T>C		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.489+23928T>C		intron_variant	Intron 4 of 4	1
LINC00907	ENST00000585639.5	n.631+23928T>C		intron_variant	Intron 5 of 6	1
LINC00907	ENST00000591381.5	n.472+23928T>C		intron_variant	Intron 4 of 4	1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38671 AN: 152044 Hom.: 6248 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.255 AC: 38743 AN: 152162 Hom.: 6271 Cov.: 33 AF XY: 0.256 AC XY: 19025 AN XY: 74388

African (AFR) AF: 0.410 AC: 17027 AN: 41490

American (AMR) AF: 0.293 AC: 4477 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 685 AN: 3466

East Asian (EAS) AF: 0.616 AC: 3185 AN: 5172

South Asian (SAS) AF: 0.200 AC: 966 AN: 4820

European-Finnish (FIN) AF: 0.126 AC: 1334 AN: 10606

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.152 AC: 10351 AN: 68006

Other (OTH) AF: 0.246 AC: 521 AN: 2116

Alfa AF: 0.194 Hom.: 9185

Bravo AF: 0.278

Asia WGS AF: 0.418 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.45
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7235528; hg19: chr18-40058882;