rs696891

Variant names:

• chr5-61608734-A-G
• rs696891
• ENST00000797197.1:n.125-1893A>G

Variant summary

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

The ENST00000797197.1(LINC03122):​n.125-1893A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,096 control chromosomes in the GnomAD database, including 27,622 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 0.58 (27622 hom., cov: 32)
• Consequence: LINC03122 ENST00000797197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772
• Publications: 3 publications found

Genes affected

LINC03122 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797197.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03122	ENST00000797197.1		n.125-1893A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87417 AN: 151980 Hom.: 27587 Cov.: 32

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.555

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.575 AC: 87495 AN: 152096 Hom.: 27622 Cov.: 32 AF XY: 0.563 AC XY: 41902 AN XY: 74364

African (AFR) AF: 0.848 AC: 35196 AN: 41500

American (AMR) AF: 0.423 AC: 6468 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1986 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2026 AN: 5170

South Asian (SAS) AF: 0.338 AC: 1629 AN: 4820

European-Finnish (FIN) AF: 0.405 AC: 4273 AN: 10562

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34090 AN: 67970

Other (OTH) AF: 0.551 AC: 1165 AN: 2116

Alfa AF: 0.521 Hom.: 3804

Bravo AF: 0.589

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	18
DANN	Benign	0.70
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs696891; hg19: chr5-60904561;