rs10502782

Positions:

• chr18-42305834-G-A
• chr18-42305834-G-C

Variant summary

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

The NR_046174.2(LINC00907):​n.403-29250G>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 0.0753 in 151,946 control chromosomes in the GnomAD database, including 1,231 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 0.075 (1231 hom., cov: 32)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00907	NR_046174.2	n.403-29250G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000589068.5	n.368-29250G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11403 AN: 151828 Hom.: 1221 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00343

Gnomad OTH AF: 0.0634

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

GnomAD4 genome AF: 0.0753 AC: 11446 AN: 151946 Hom.: 1231 Cov.: 32 AF XY: 0.0776 AC XY: 5762 AN XY: 74272

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.00865

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.0375

Gnomad4 FIN AF: 0.0234

Gnomad4 NFE AF: 0.00344

Gnomad4 OTH AF: 0.0694

Alfa AF: 0.0162 Hom.: 153

Bravo AF: 0.0865

Asia WGS AF: 0.246 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502782; hg19: chr18-39885799;