2-41943714-T-C

Variant names:

• chr2-41943714-T-C
• rs7556683
• ENST00000378711.2:n.475+3781A>G

Variant summary

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

The ENST00000378711.2(LINC02898):​n.475+3781A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,916 control chromosomes in the GnomAD database, including 10,254 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 0.36 (10254 hom., cov: 32)
• Consequence: LINC02898 ENST00000378711.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 1 publications found

Genes affected

LINC02898 (HGNC:42966): (long intergenic non-protein coding RNA 2898)

ENSG00000299946 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000378711.2. 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
	LINC02898	NR_161189.1		n.478+3781A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02898	ENST00000378711.2	TSL:2	n.475+3781A>G		intron	N/A
	LINC02898	ENST00000649862.1		n.716+3781A>G		intron	N/A
	ENSG00000299946	ENST00000767619.1		n.180+5076T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55112 AN: 151798 Hom.: 10240 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.363 AC: 55156 AN: 151916 Hom.: 10254 Cov.: 32 AF XY: 0.368 AC XY: 27334 AN XY: 74220

African (AFR) AF: 0.310 AC: 12825 AN: 41412

American (AMR) AF: 0.348 AC: 5307 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3464

East Asian (EAS) AF: 0.448 AC: 2313 AN: 5160

South Asian (SAS) AF: 0.334 AC: 1604 AN: 4808

European-Finnish (FIN) AF: 0.452 AC: 4766 AN: 10536

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 26023 AN: 67968

Other (OTH) AF: 0.353 AC: 747 AN: 2116

Alfa AF: 0.376 Hom.: 5658

Bravo AF: 0.348

Asia WGS AF: 0.403 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.39
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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: rs7556683;

hg19: chr2-42170854;