5-61596378-G-A

Variant names:

• chr5-61596378-G-A
• rs381034
• ENST00000797197.1:n.124+542G>A

Variant summary

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

The ENST00000797197.1(LINC03122):​n.124+542G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,112 control chromosomes in the GnomAD database, including 5,191 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 0.26 (5191 hom., cov: 32)
• Consequence: LINC03122 ENST00000797197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 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.124+542G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39018 AN: 151994 Hom.: 5197 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.256 AC: 39009 AN: 152112 Hom.: 5191 Cov.: 32 AF XY: 0.251 AC XY: 18649 AN XY: 74352

African (AFR) AF: 0.210 AC: 8713 AN: 41480

American (AMR) AF: 0.227 AC: 3474 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1085 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1249 AN: 5180

South Asian (SAS) AF: 0.187 AC: 901 AN: 4824

European-Finnish (FIN) AF: 0.228 AC: 2415 AN: 10572

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20299 AN: 67980

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.285 Hom.: 27146

Bravo AF: 0.255

Asia WGS AF: 0.193 AC: 673 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	2.0
DANN	Benign	0.54
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs381034; hg19: chr5-60892205;