rs4699982

Variant names:

• chr5-61729255-A-T
• rs4699982
• ENST00000507461.2:n.140-19347A>T

Variant summary

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

The ENST00000510414.4(LINC03122):​n.405-791A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,086 control chromosomes in the GnomAD database, including 3,761 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 0.21 (3761 hom., cov: 32)
• Consequence: LINC03122 ENST00000510414.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510414.4. 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
	LINC03122	NR_126524.1		n.384-791A>T		intron	N/A
	LINC03122	NR_126525.1		n.67-791A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03122	ENST00000507461.2	TSL:4	n.140-19347A>T		intron	N/A
	LINC03122	ENST00000510414.4	TSL:3	n.405-791A>T		intron	N/A
	LINC03122	ENST00000511407.1	TSL:4	n.67-791A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32387 AN: 151968 Hom.: 3759 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.213 AC: 32404 AN: 152086 Hom.: 3761 Cov.: 32 AF XY: 0.212 AC XY: 15752 AN XY: 74354

African (AFR) AF: 0.300 AC: 12455 AN: 41470

American (AMR) AF: 0.171 AC: 2614 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3472

East Asian (EAS) AF: 0.116 AC: 600 AN: 5168

South Asian (SAS) AF: 0.181 AC: 871 AN: 4814

European-Finnish (FIN) AF: 0.195 AC: 2059 AN: 10578

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12431 AN: 67980

Other (OTH) AF: 0.216 AC: 456 AN: 2112

Alfa AF: 0.206 Hom.: 420

Bravo AF: 0.212

Asia WGS AF: 0.185 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.54
PhyloP100		-0.043

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: rs4699982;

hg19: chr5-61025082;