rs9358578

chr6-22702418-G-A

Variant summary

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

The NR_134614.1(LINC03005):n.204+15303C>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 0.15 in 152,082 control chromosomes in the GnomAD database, including 2,277 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 0.15 (2277 hom., cov: 31)
• Consequence: LINC03005 NR_134614.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

Genes affected

LINC03005 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03005	NR_134614.1	n.204+15303C>T		intron_variant, non_coding_transcript_variant
LINC03005	NR_134613.1	n.204+15303C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22804 AN: 151964 Hom.: 2278 Cov.: 31

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.0507

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.150 AC: 22805 AN: 152082 Hom.: 2277 Cov.: 31 AF XY: 0.149 AC XY: 11087 AN XY: 74324

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.178

Alfa AF: 0.170 Hom.: 410

Bravo AF: 0.140

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.68
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9358578; hg19: chr6-22702647;