rs12606301

chr18-42443817-G-A

Variant summary

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

The NR_046174.2(LINC00907):n.623-10115G>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 0.142 in 150,866 control chromosomes in the GnomAD database, including 2,060 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 0.14 (2060 hom., cov: 28)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00907	NR_046174.2	n.623-10115G>A		intron_variant, non_coding_transcript_variant
LINC00907	NR_046454.1	n.403-10115G>A		intron_variant, non_coding_transcript_variant
LINC00907	NR_046456.1	n.714-10115G>A		intron_variant, non_coding_transcript_variant
LINC00907	NR_046457.1	n.494-10115G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000589068.5	n.588-10115G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21449 AN: 150748 Hom.: 2054 Cov.: 28

Gnomad AFR AF: 0.0870

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.142 AC: 21468 AN: 150866 Hom.: 2060 Cov.: 28 AF XY: 0.144 AC XY: 10634 AN XY: 73594

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.0950

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.163

Alfa AF: 0.146 Hom.: 2294

Bravo AF: 0.153

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	-0.89
Cadd	Benign	0.17
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12606301; hg19: chr18-40023782;