5-61753340-G-A

Variant names:

• chr5-61753340-G-A
• rs2030889
• ENST00000507461.2:n.542+1570G>A

Variant summary

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

The ENST00000507461.2(LINC03122):​n.542+1570G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,130 control chromosomes in the GnomAD database, including 1,774 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 0.15 (1774 hom., cov: 32)
• Consequence: LINC03122 ENST00000507461.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• 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]

LOC124900983 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900983	XR_007058782.1	n.301+1570G>A		intron_variant	Intron 3 of 3
LOC124900983	XR_007058783.1	n.409-2492G>A		intron_variant	Intron 3 of 4
LOC124900983	XR_007058784.1	n.201-2492G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03122	ENST00000507461.2	n.542+1570G>A		intron_variant	Intron 4 of 4	4
LINC03122	ENST00000655479.2	n.451-2492G>A		intron_variant	Intron 4 of 4
LINC03122	ENST00000656556.1	n.515+1570G>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22345 AN: 152012 Hom.: 1777 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.147 AC: 22351 AN: 152130 Hom.: 1774 Cov.: 32 AF XY: 0.144 AC XY: 10673 AN XY: 74358

African (AFR) AF: 0.118 AC: 4895 AN: 41506

American (AMR) AF: 0.109 AC: 1669 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3470

East Asian (EAS) AF: 0.183 AC: 944 AN: 5158

South Asian (SAS) AF: 0.114 AC: 549 AN: 4814

European-Finnish (FIN) AF: 0.144 AC: 1524 AN: 10592

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11769 AN: 67990

Other (OTH) AF: 0.150 AC: 316 AN: 2110

Alfa AF: 0.162 Hom.: 6589

Bravo AF: 0.145

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.69
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2030889; hg19: chr5-61049167;