chr6-169158234-A-T

Position:

• chr6-169158234-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_132623.1(LINC01615):​n.570T>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 NR_132623.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01615	NR_132623.1	n.570T>A		non_coding_transcript_exon_variant	2/2
LINC01615	NR_132622.1	n.630T>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01615	ENST00000657431.3	n.588T>A		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR exome AF: 0.0796

Gnomad4 AMR exome AF: 0.0199

Gnomad4 ASJ exome AF: 0.0199

Gnomad4 EAS exome AF: 0.0196

Gnomad4 SAS exome AF: 0.00171

Gnomad4 FIN exome AF: 0.00223

Gnomad4 NFE exome AF: 0.0129

Gnomad4 OTH exome AF: 0.0256

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

Gnomad4 AFR AF: 0.0912

Gnomad4 AMR AF: 0.0282

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0200

Gnomad4 SAS AF: 0.00663

Gnomad4 FIN AF: 0.00273

Gnomad4 NFE AF: 0.0149

Gnomad4 OTH AF: 0.0432

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	12
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485333; hg19: chr6-169558329;