chr3-25871924-T-C

Position:

• chr3-25871924-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_034055.1(LINC00692):​n.224-28A>G variant causes a intron, non coding transcript 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 NR_034055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00692	NR_034055.1	n.224-28A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00692	ENST00000451284.6	n.277-28A>G		intron_variant, non_coding_transcript_variant		1
LINC00692	ENST00000655652.1	n.234-28A>G		intron_variant, non_coding_transcript_variant
LINC00692	ENST00000496997.1	n.193-28A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 NFE exome AF: 1.00

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

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.852

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.812

Alfa AF: 0.824 Hom.: 104809

Bravo AF: 0.787

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4293672; hg19: chr3-25913415;