chr2-19121042-T-C

Variant names:

• chr2-19121042-T-C
• rs12710696
• ENST00000418165.5:n.351+4210A>G

Variant summary

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

The ENST00000449124.1(LINC01376):​n.241+4210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,002 control chromosomes in the GnomAD database, including 26,755 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 0.59 (26755 hom., cov: 32)
• Consequence: LINC01376 ENST00000449124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937
• Publications: 69 publications found

Genes affected

LINC01376 (HGNC:50637): (long intergenic non-protein coding RNA 1376)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449124.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01376	ENST00000418165.5	TSL:4	n.351+4210A>G		intron	N/A
	LINC01376	ENST00000432142.6	TSL:4	n.637+4210A>G		intron	N/A
	LINC01376	ENST00000449124.1	TSL:2	n.241+4210A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88960 AN: 151884 Hom.: 26732 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.586 AC: 89031 AN: 152002 Hom.: 26755 Cov.: 32 AF XY: 0.585 AC XY: 43435 AN XY: 74280

African (AFR) AF: 0.469 AC: 19460 AN: 41464

American (AMR) AF: 0.672 AC: 10261 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1606 AN: 3468

East Asian (EAS) AF: 0.697 AC: 3595 AN: 5158

South Asian (SAS) AF: 0.425 AC: 2042 AN: 4806

European-Finnish (FIN) AF: 0.647 AC: 6825 AN: 10556

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43188 AN: 67962

Other (OTH) AF: 0.607 AC: 1281 AN: 2112

Alfa AF: 0.619 Hom.: 64483

Bravo AF: 0.587

Asia WGS AF: 0.568 AC: 1974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs12710696; hg19: chr2-19320803;