3-25872392-A-G

Variant names:

• chr3-25872392-A-G
• rs6551000
• ENST00000451284.6:n.199T>C

Variant summary

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

The ENST00000451284.6(LINC00692):​n.199T>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 0.665 in 152,128 control chromosomes in the GnomAD database, including 38,475 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 0.67 (38465 hom., cov: 33)
  • Exomes 𝑓: 0.92 (10 hom.)
• Consequence: LINC00692 ENST00000451284.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 publications found

Genes affected

LINC00692 (HGNC:27708): (long intergenic non-protein coding RNA 692)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451284.6. 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
	LINC00692	NR_034055.1		n.146T>C		non_coding_transcript_exon	Exon 2 of 8

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00692	ENST00000451284.6	TSL:1	n.199T>C		non_coding_transcript_exon	Exon 2 of 8
	LINC00692	ENST00000496997.1	TSL:5	n.115T>C		non_coding_transcript_exon	Exon 2 of 5
	LINC00692	ENST00000655652.1		n.156T>C		non_coding_transcript_exon	Exon 2 of 8

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101163 AN: 151986 Hom.: 38450 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.713

GnomAD4 exome AF: 0.917 AC: 22 AN: 24 Hom.: 10 Cov.: 0 AF XY: 0.950 AC XY: 19 AN XY: 20

African (AFR) AF: 1.00 AC: 2 AN: 2

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) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.944 AC: 17 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.665 AC: 101206 AN: 152104 Hom.: 38465 Cov.: 33 AF XY: 0.672 AC XY: 49979 AN XY: 74368

African (AFR) AF: 0.267 AC: 11080 AN: 41468

American (AMR) AF: 0.799 AC: 12207 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2924 AN: 3468

East Asian (EAS) AF: 0.961 AC: 4969 AN: 5170

South Asian (SAS) AF: 0.743 AC: 3572 AN: 4810

European-Finnish (FIN) AF: 0.815 AC: 8630 AN: 10594

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55358 AN: 68000

Other (OTH) AF: 0.716 AC: 1514 AN: 2114

Alfa AF: 0.785 Hom.: 119751

Bravo AF: 0.648

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.51
DANN	Benign	0.76
PhyloP100		-1.1
Mutation Taster		=300/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6551000; hg19: chr3-25913883;