rs9304270

chr18-42357544-C-T

Variant summary

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

The NR_046174.2(LINC00907):n.622+22241C>T 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 0.19 in 151,632 control chromosomes in the GnomAD database, including 3,178 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 0.19 (3178 hom., cov: 31)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00907	NR_046174.2	n.622+22241C>T		intron_variant, non_coding_transcript_variant
LINC00907	NR_046454.1	n.403-96388C>T		intron_variant, non_coding_transcript_variant
LINC00907	NR_046456.1	n.713+22241C>T		intron_variant, non_coding_transcript_variant
LINC00907	NR_046457.1	n.493+67950C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000589068.5	n.587+22241C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28714 AN: 151524 Hom.: 3164 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.190 AC: 28777 AN: 151632 Hom.: 3178 Cov.: 31 AF XY: 0.189 AC XY: 14000 AN XY: 74022

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.192

Alfa AF: 0.148 Hom.: 3099

Bravo AF: 0.200

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.87
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9304270; hg19: chr18-39937509;