rs17782339

Variant names:

• chr3-163249233-A-G
• rs17782339
• ENST00000470546.5:n.158+29277T>C

Variant summary

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

The ENST00000671181.1(LINC01192):​n.645T>C 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 0.331 in 150,670 control chromosomes in the GnomAD database, including 8,634 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 0.33 (8634 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: LINC01192 ENST00000671181.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 2 publications found

Genes affected

LINC01192 (HGNC:37197): (long intergenic non-protein coding RNA 1192)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671181.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01192	NR_033945.1		n.158+29277T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01192	ENST00000470546.5	TSL:1	n.158+29277T>C		intron	N/A
	LINC01192	ENST00000671181.1		n.645T>C		non_coding_transcript_exon	Exon 5 of 5
	LINC01192	ENST00000462928.5	TSL:3	n.65-29046T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.331 AC: 49898 AN: 150552 Hom.: 8634 Cov.: 30

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.376

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.331 AC: 49901 AN: 150670 Hom.: 8634 Cov.: 30 AF XY: 0.329 AC XY: 24193 AN XY: 73576

African (AFR) AF: 0.282 AC: 11628 AN: 41252

American (AMR) AF: 0.360 AC: 5420 AN: 15038

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1275 AN: 3448

East Asian (EAS) AF: 0.581 AC: 2944 AN: 5070

South Asian (SAS) AF: 0.243 AC: 1166 AN: 4802

European-Finnish (FIN) AF: 0.309 AC: 3249 AN: 10514

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23050 AN: 67246

Other (OTH) AF: 0.373 AC: 781 AN: 2096

Alfa AF: 0.315 Hom.: 981

Bravo AF: 0.340

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.58
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17782339;

hg19: chr3-162967021;