rs9466427

chr6-22660103-T-G

Variant summary

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

The NR_134614.1(LINC03005):n.249+6892A>C 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 0.826 in 152,124 control chromosomes in the GnomAD database, including 52,501 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 0.83 (52501 hom., cov: 32)
• Consequence: LINC03005 NR_134614.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

LINC03005 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03005	NR_134614.1	n.249+6892A>C		intron_variant, non_coding_transcript_variant
LINC03005	NR_134613.1	n.205-5399A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125529 AN: 152006 Hom.: 52442 Cov.: 32

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.826 AC: 125647 AN: 152124 Hom.: 52501 Cov.: 32 AF XY: 0.826 AC XY: 61429 AN XY: 74334

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.810

Alfa AF: 0.802 Hom.: 7995

Bravo AF: 0.839

Asia WGS AF: 0.739 AC: 2572 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.24
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9466427; hg19: chr6-22660332;