chr18-42478917-T-C

Position:

• chr18-42478917-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046174.2(LINC00907):​n.872+23928T>C variant causes a intron, non coding transcript 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 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896

Genes affected

LINC00907 (HGNC:44327): (long intergenic non-protein coding RNA 907)

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00907	NR_046174.2	n.872+23928T>C		intron_variant, non_coding_transcript_variant
LINC00907	NR_046454.1	n.652+23928T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000585627.5	n.489+23928T>C		intron_variant, non_coding_transcript_variant		1
LINC00907	ENST00000585639.5	n.631+23928T>C		intron_variant, non_coding_transcript_variant		1
LINC00907	ENST00000589068.5	n.837+23928T>C		intron_variant, non_coding_transcript_variant		2
LINC00907	ENST00000591381.5	n.472+23928T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.246

Alfa AF: 0.174 Hom.: 4239

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7235528; hg19: chr18-40058882;