ENST00000507461.2:n.140-23607G>A

Variant names:

• chr5-61724995-G-A
• rs10514917
• ENST00000507461.2:n.140-23607G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000507461.2(LINC03122):​n.140-23607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 152,172 control chromosomes in the GnomAD database, including 84 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 0.022 (84 hom., cov: 32)
• Consequence: LINC03122 ENST00000507461.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 1 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=-0.82).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0224 (3405/152172) while in subpopulation AFR AF = 0.0477 (1980/41476). AF 95% confidence interval is 0.046. There are 84 homozygotes in GnomAd4. There are 1793 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 84 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03122	NR_126524.1	n.384-5051G>A		intron_variant	Intron 3 of 3
LINC03122	NR_126525.1	n.67-5051G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03122	ENST00000507461.2	n.140-23607G>A		intron_variant	Intron 1 of 4	4
LINC03122	ENST00000510414.4	n.405-5051G>A		intron_variant	Intron 3 of 3	3
LINC03122	ENST00000511407.1	n.67-5051G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3390 AN: 152052 Hom.: 83 Cov.: 32

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0102

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00794

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0224 AC: 3405 AN: 152172 Hom.: 84 Cov.: 32 AF XY: 0.0241 AC XY: 1793 AN XY: 74392

African (AFR) AF: 0.0477 AC: 1980 AN: 41476

American (AMR) AF: 0.0103 AC: 157 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3468

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5178

South Asian (SAS) AF: 0.0328 AC: 158 AN: 4816

European-Finnish (FIN) AF: 0.0401 AC: 425 AN: 10600

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.00794 AC: 540 AN: 68016

Other (OTH) AF: 0.0227 AC: 48 AN: 2114

Alfa AF: 0.0116 Hom.: 16

Bravo AF: 0.0208

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.80
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10514917; hg19: chr5-61020822;