6-169158234-A-T

Variant names:

• chr6-169158234-A-T
• rs10485333
• ENST00000439703.1:n.505T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000439703.1(LINC01615):​n.505T>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 0.024 in 386,742 control chromosomes in the GnomAD database, including 250 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 0.037 (187 hom., cov: 33)
  • Exomes 𝑓: 0.016 (63 hom.)
• Consequence: LINC01615 ENST00000439703.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 3 publications found

Genes affected

LINC01615 (HGNC:51898): (long intergenic non-protein coding RNA 1615)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0888 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439703.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01615	NR_132622.1		n.630T>A		non_coding_transcript_exon	Exon 4 of 4
	LINC01615	NR_132623.1		n.570T>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01615	ENST00000439703.1	TSL:2	n.505T>A		non_coding_transcript_exon	Exon 2 of 2
	LINC01615	ENST00000634877.2	TSL:5	n.735T>A		non_coding_transcript_exon	Exon 3 of 3
	LINC01615	ENST00000651190.1		n.561T>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0365 AC: 5562 AN: 152192 Hom.: 184 Cov.: 33

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0283

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.00273

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0149

Gnomad OTH AF: 0.0446

GnomAD4 exome AF: 0.0158 AC: 3715 AN: 234432 Hom.: 63 Cov.: 0 AF XY: 0.0149 AC XY: 1759 AN XY: 118230

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0796 AC: 546 AN: 6856

American (AMR) AF: 0.0199 AC: 137 AN: 6900

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 174 AN: 8734

East Asian (EAS) AF: 0.0196 AC: 441 AN: 22512

South Asian (SAS) AF: 0.00171 AC: 5 AN: 2918

European-Finnish (FIN) AF: 0.00223 AC: 45 AN: 20168

Middle Eastern (MID) AF: 0.0274 AC: 33 AN: 1204

European-Non Finnish (NFE) AF: 0.0129 AC: 1936 AN: 149594

Other (OTH) AF: 0.0256 AC: 398 AN: 15546

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0366 AC: 5578 AN: 152310 Hom.: 187 Cov.: 33 AF XY: 0.0357 AC XY: 2656 AN XY: 74484

African (AFR) AF: 0.0912 AC: 3792 AN: 41558

American (AMR) AF: 0.0282 AC: 431 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3468

East Asian (EAS) AF: 0.0200 AC: 104 AN: 5188

South Asian (SAS) AF: 0.00663 AC: 32 AN: 4824

European-Finnish (FIN) AF: 0.00273 AC: 29 AN: 10620

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0149 AC: 1014 AN: 68034

Other (OTH) AF: 0.0432 AC: 91 AN: 2108

Alfa AF: 0.00713 Hom.: 2

Bravo AF: 0.0427

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	12
DANN	Benign	0.91
PhyloP100		1.5
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10485333; hg19: chr6-169558329;