rs1346987

chr18-42522676-C-Achr18-42522676-C-G

Variant summary

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

The NR_046174.2(LINC00907):n.873-52117C>A 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 0.207 in 151,922 control chromosomes in the GnomAD database, including 4,021 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 0.21 (4021 hom., cov: 32)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00907	NR_046174.2	n.873-52117C>A		intron_variant, non_coding_transcript_variant
LINC00907	NR_046454.1	n.703+6507C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000585639.5	n.682+6507C>A		intron_variant, non_coding_transcript_variant		1
LINC00907	ENST00000589068.5	n.838-52117C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31375 AN: 151804 Hom.: 4010 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.207 AC: 31423 AN: 151922 Hom.: 4021 Cov.: 32 AF XY: 0.206 AC XY: 15312 AN XY: 74264

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.0945

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.202

Alfa AF: 0.153 Hom.: 3261

Bravo AF: 0.227

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	-0.90
Cadd	Benign	0.87
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1346987; hg19: chr18-40102641;