chr3-25871924-T-C

Variant names:

• chr3-25871924-T-C
• rs4293672
• ENST00000451284.6:n.277-28A>G

Variant summary

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

The ENST00000451284.6(LINC00692):​n.277-28A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,104 control chromosomes in the GnomAD database, including 47,838 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 0.79 (47837 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LINC00692 ENST00000451284.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 2 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=-0.9).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00692	NR_034055.1		n.224-28A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00692	ENST00000451284.6	TSL:1	n.277-28A>G		intron	N/A
	LINC00692	ENST00000496997.1	TSL:5	n.193-28A>G		intron	N/A
	LINC00692	ENST00000655652.1		n.234-28A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119808 AN: 151984 Hom.: 47799 Cov.: 33

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.810

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 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) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.788 AC: 119896 AN: 152102 Hom.: 47837 Cov.: 33 AF XY: 0.791 AC XY: 58829 AN XY: 74360

African (AFR) AF: 0.662 AC: 27426 AN: 41448

American (AMR) AF: 0.861 AC: 13162 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2955 AN: 3468

East Asian (EAS) AF: 0.962 AC: 4973 AN: 5172

South Asian (SAS) AF: 0.757 AC: 3658 AN: 4832

European-Finnish (FIN) AF: 0.828 AC: 8761 AN: 10582

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56273 AN: 67988

Other (OTH) AF: 0.812 AC: 1719 AN: 2116

Alfa AF: 0.818 Hom.: 213091

Bravo AF: 0.787

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4293672; hg19: chr3-25913415;