2-41888764-T-G

Variant names:

• chr2-41888764-T-G
• rs4358170
• ENST00000442214.1:n.224-3765T>G

Variant summary

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

The ENST00000442214.1(LINC01913):​n.224-3765T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 151,874 control chromosomes in the GnomAD database, including 33,720 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 0.67 (33720 hom., cov: 31)
• Consequence: LINC01913 ENST00000442214.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 2 publications found

Genes affected

LINC01913 (HGNC:52732): (long intergenic non-protein coding RNA 1913)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442214.1. 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
	LINC01913	NR_033996.1		n.225-1587T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01913	ENST00000442214.1	TSL:1	n.224-3765T>G		intron	N/A
	LINC01913	ENST00000398796.4	TSL:2	n.226-1587T>G		intron	N/A
	LINC01913	ENST00000649168.1		n.669-1587T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100945 AN: 151756 Hom.: 33682 Cov.: 31

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.665 AC: 101038 AN: 151874 Hom.: 33720 Cov.: 31 AF XY: 0.669 AC XY: 49658 AN XY: 74216

African (AFR) AF: 0.609 AC: 25207 AN: 41364

American (AMR) AF: 0.710 AC: 10853 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2050 AN: 3470

East Asian (EAS) AF: 0.657 AC: 3379 AN: 5142

South Asian (SAS) AF: 0.717 AC: 3451 AN: 4816

European-Finnish (FIN) AF: 0.732 AC: 7717 AN: 10542

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.679 AC: 46171 AN: 67958

Other (OTH) AF: 0.664 AC: 1395 AN: 2102

Alfa AF: 0.620 Hom.: 3318

Bravo AF: 0.659

Asia WGS AF: 0.738 AC: 2565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.60
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs4358170; hg19: chr2-42115904;