rs17718122

Positions:

• chr7-76580142-A-G
• chr7-76580142-A-T

Variant summary

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

The NR_029411.1(LINC03009):​n.624+28620A>G 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 0.25 in 151,624 control chromosomes in the GnomAD database, including 5,279 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 (5279 hom., cov: 31)
• Consequence: LINC03009 NR_029411.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

LINC03009 (HGNC:56134): (long intergenic non-protein coding RNA 3009)

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 (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03009	NR_029411.1	n.624+28620A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03009	ENST00000418663.5	n.605+28620A>G		intron_variant, non_coding_transcript_variant		1
LINC03009	ENST00000450661.1	n.604+28620A>G		intron_variant, non_coding_transcript_variant		1
LINC03009	ENST00000423084.1	n.305+28620A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37857 AN: 151504 Hom.: 5273 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.250 AC: 37862 AN: 151624 Hom.: 5279 Cov.: 31 AF XY: 0.244 AC XY: 18102 AN XY: 74124

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.292

Alfa AF: 0.300 Hom.: 10587

Bravo AF: 0.249

Asia WGS AF: 0.115 AC: 402 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	12
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17718122; hg19: chr7-76209459;