rs4706205

Positions:

• chr6-84474855-A-T

Variant summary

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

The NR_132100.1(LINC01611):​n.75T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,838 control chromosomes in the GnomAD database, including 18,716 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 0.49 (18715 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: LINC01611 NR_132100.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

Genes affected

LINC01611 (HGNC:51791): (long intergenic non-protein coding RNA 1611)

LOC107986620 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01611	NR_132100.1	n.75T>A		non_coding_transcript_exon_variant	1/5
LOC107986620	XR_001744235.2	n.191+21528A>T		intron_variant, non_coding_transcript_variant
LOC107986620	XR_001744236.1	n.134+21528A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01611	ENST00000454172.5	n.135-30404T>A		intron_variant, non_coding_transcript_variant		3
LINC01611	ENST00000428896.1	n.75T>A		non_coding_transcript_exon_variant	1/4	5

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74295 AN: 151716 Hom.: 18704 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.524

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.490 AC: 74343 AN: 151834 Hom.: 18715 Cov.: 32 AF XY: 0.491 AC XY: 36441 AN XY: 74176

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.525

Alfa AF: 0.505 Hom.: 2441

Bravo AF: 0.487

Asia WGS AF: 0.599 AC: 2077 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4706205; hg19: chr6-85184573;