5-61752940-T-A

Variant names:

• chr5-61752940-T-A
• rs2030891
• ENST00000507461.2:n.542+1170T>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+1170T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,176 control chromosomes in the GnomAD database, including 43,142 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 0.75 (43142 hom., cov: 32)
• Consequence: LINC03122 ENST00000507461.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• 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]

LOC124900983 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900983	XR_007058782.1	n.301+1170T>A		intron_variant	Intron 3 of 3
LOC124900983	XR_007058783.1	n.408+2396T>A		intron_variant	Intron 3 of 4
LOC124900983	XR_007058784.1	n.201-2892T>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+1170T>A		intron_variant	Intron 4 of 4	4
LINC03122	ENST00000655479.2	n.450+2396T>A		intron_variant	Intron 4 of 4
LINC03122	ENST00000656556.1	n.515+1170T>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113382 AN: 152058 Hom.: 43107 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.746 AC: 113470 AN: 152176 Hom.: 43142 Cov.: 32 AF XY: 0.739 AC XY: 54934 AN XY: 74376

African (AFR) AF: 0.882 AC: 36625 AN: 41542

American (AMR) AF: 0.630 AC: 9636 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2708 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2250 AN: 5174

South Asian (SAS) AF: 0.679 AC: 3268 AN: 4816

European-Finnish (FIN) AF: 0.706 AC: 7469 AN: 10572

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49038 AN: 67996

Other (OTH) AF: 0.750 AC: 1584 AN: 2112

Alfa AF: 0.735 Hom.: 5177

Bravo AF: 0.743

Asia WGS AF: 0.579 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.034
DANN	Benign	0.33
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2030891; hg19: chr5-61048767;