chr5-61611974-T-C

Variant names:

• chr5-61611974-T-C
• rs895381
• ENST00000654772.1:n.207+1259T>C

Variant summary

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

The ENST00000654772.1(LINC03122):​n.207+1259T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,086 control chromosomes in the GnomAD database, including 24,094 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 0.55 (24094 hom., cov: 32)
• Consequence: LINC03122 ENST00000654772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654772.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03122	ENST00000654772.1		n.207+1259T>C		intron	N/A
	LINC03122	ENST00000657803.1		n.171+1259T>C		intron	N/A
	LINC03122	ENST00000659478.1		n.207+1259T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83862 AN: 151968 Hom.: 24075 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.552 AC: 83917 AN: 152086 Hom.: 24094 Cov.: 32 AF XY: 0.562 AC XY: 41753 AN XY: 74342

African (AFR) AF: 0.395 AC: 16402 AN: 41482

American (AMR) AF: 0.668 AC: 10213 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1887 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3909 AN: 5172

South Asian (SAS) AF: 0.735 AC: 3550 AN: 4828

European-Finnish (FIN) AF: 0.658 AC: 6961 AN: 10572

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39055 AN: 67968

Other (OTH) AF: 0.583 AC: 1229 AN: 2108

Alfa AF: 0.577 Hom.: 13263

Bravo AF: 0.544

Asia WGS AF: 0.734 AC: 2553 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	0.94
DANN	Benign	0.50
PhyloP100		-0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs895381;

hg19: chr5-60907801;