2-131670848-T-C

Variant names:

• chr2-131670848-T-C
• rs4850234
• ENST00000652878.1:n.231-13861T>C

Variant summary

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

The ENST00000652878.1(LINC03124):​n.231-13861T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,238 control chromosomes in the GnomAD database, including 62,299 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 0.89 (62299 hom., cov: 32)
• Consequence: LINC03124 ENST00000652878.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

Genes affected

LINC03124 (HGNC:25077): (long intergenic non-protein coding RNA 3124)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652878.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03124	ENST00000652878.1		n.231-13861T>C		intron	N/A
	LINC03124	ENST00000779756.1		n.208-17318T>C		intron	N/A
	LINC03124	ENST00000779757.1		n.239-13861T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135201 AN: 152120 Hom.: 62275 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.889 AC: 135276 AN: 152238 Hom.: 62299 Cov.: 32 AF XY: 0.893 AC XY: 66481 AN XY: 74448

African (AFR) AF: 0.613 AC: 25427 AN: 41476

American (AMR) AF: 0.961 AC: 14701 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3456 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5184

South Asian (SAS) AF: 0.998 AC: 4820 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10621 AN: 10626

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67920 AN: 68030

Other (OTH) AF: 0.922 AC: 1948 AN: 2112

Alfa AF: 0.964 Hom.: 59737

Bravo AF: 0.872

Asia WGS AF: 0.978 AC: 3401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4850234; hg19: chr2-132428421;