ENST00000778649.1:n.183+32850G>C

Variant names:

• chr2-194317766-G-C
• rs1376702
• ENST00000778649.1:n.183+32850G>C

Variant summary

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

The ENST00000778649.1(LINC01821):​n.183+32850G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,030 control chromosomes in the GnomAD database, including 63,687 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 0.91 (63687 hom., cov: 31)
• Consequence: LINC01821 ENST00000778649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 1 publications found

Genes affected

LINC01821 (HGNC:52626): (long intergenic non-protein coding RNA 1821)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01821	ENST00000778649.1	n.183+32850G>C		intron_variant	Intron 1 of 4
LINC01821	ENST00000778650.1	n.180+32850G>C		intron_variant	Intron 1 of 3
LINC01821	ENST00000778651.1	n.182+32850G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138894 AN: 151912 Hom.: 63652 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.914 AC: 138975 AN: 152030 Hom.: 63687 Cov.: 31 AF XY: 0.916 AC XY: 68048 AN XY: 74322

African (AFR) AF: 0.864 AC: 35832 AN: 41470

American (AMR) AF: 0.903 AC: 13759 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.958 AC: 3322 AN: 3466

East Asian (EAS) AF: 0.844 AC: 4355 AN: 5158

South Asian (SAS) AF: 0.954 AC: 4606 AN: 4828

European-Finnish (FIN) AF: 0.968 AC: 10271 AN: 10612

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.938 AC: 63697 AN: 67942

Other (OTH) AF: 0.922 AC: 1946 AN: 2110

Alfa AF: 0.929 Hom.: 8159

Bravo AF: 0.904

Asia WGS AF: 0.871 AC: 3027 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs1376702; hg19: chr2-195182490;