rs678385

Positions:

• chr6-137671413-A-G
• chr6-137671413-A-T

Variant summary

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

The NR_125867.1(LINC03004):​n.95-607A>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 0.537 in 151,966 control chromosomes in the GnomAD database, including 21,895 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 0.54 (21895 hom., cov: 32)
• Consequence: LINC03004 NR_125867.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

Genes affected

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03004	NR_125867.1	n.95-607A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03004	ENST00000642830.1	n.426-607A>G		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000691587.1	n.133-607A>G		intron_variant, non_coding_transcript_variant
LINC03004	ENST00000692965.2	n.266-607A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81497 AN: 151848 Hom.: 21865 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.537 AC: 81574 AN: 151966 Hom.: 21895 Cov.: 32 AF XY: 0.532 AC XY: 39516 AN XY: 74266

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.522

Alfa AF: 0.516 Hom.: 2846

Bravo AF: 0.548

Asia WGS AF: 0.469 AC: 1625 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs678385; hg19: chr6-137992550;