rs4706205

Variant names:

• chr6-84474855-A-T
• rs4706205
• ENST00000428896.1:n.75T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000428896.1(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 ENST00000428896.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 0 publications found

Genes affected

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

ENSG00000303044 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01611	NR_132100.1	n.75T>A		non_coding_transcript_exon_variant	Exon 1 of 5
LOC107986620	XR_001744235.2	n.191+21528A>T		intron_variant	Intron 2 of 2
LOC107986620	XR_001744236.1	n.134+21528A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01611	ENST00000428896.1	n.75T>A		non_coding_transcript_exon_variant	Exon 1 of 4	5
LINC01611	ENST00000454172.6	n.554-30404T>A		intron_variant	Intron 2 of 3	3
LINC01611	ENST00000454981.6	n.217-3951T>A		intron_variant	Intron 2 of 5	3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.369 AC: 15312 AN: 41440

American (AMR) AF: 0.511 AC: 7791 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2212 AN: 3468

East Asian (EAS) AF: 0.690 AC: 3553 AN: 5146

South Asian (SAS) AF: 0.515 AC: 2480 AN: 4816

European-Finnish (FIN) AF: 0.510 AC: 5388 AN: 10560

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35843 AN: 67856

Other (OTH) AF: 0.525 AC: 1105 AN: 2106

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs4706205; hg19: chr6-85184573;