1-190776839-T-C

Variant names:

• chr1-190776839-T-C
• rs10494642
• ENST00000413356.1:n.218-14675T>C

Variant summary

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

The ENST00000413356.1(LINC01720):​n.218-14675T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,692 control chromosomes in the GnomAD database, including 1,293 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 0.12 (1293 hom., cov: 32)
• Consequence: LINC01720 ENST00000413356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 3 publications found

Genes affected

LINC01720 (HGNC:52507): (long intergenic non-protein coding RNA 1720)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413356.1. 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
	LINC01720	NR_033922.2		n.218-14675T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01720	ENST00000413356.1	TSL:1	n.218-14675T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18239 AN: 151574 Hom.: 1291 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0501

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.120 AC: 18241 AN: 151692 Hom.: 1293 Cov.: 32 AF XY: 0.118 AC XY: 8785 AN XY: 74142

African (AFR) AF: 0.0699 AC: 2901 AN: 41490

American (AMR) AF: 0.105 AC: 1596 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 553 AN: 3458

East Asian (EAS) AF: 0.0503 AC: 260 AN: 5174

South Asian (SAS) AF: 0.0669 AC: 323 AN: 4828

European-Finnish (FIN) AF: 0.168 AC: 1780 AN: 10566

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10384 AN: 67644

Other (OTH) AF: 0.129 AC: 272 AN: 2104

Alfa AF: 0.125 Hom.: 727

Bravo AF: 0.115

Asia WGS AF: 0.0610 AC: 212 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.75
DANN	Benign	0.51
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10494642; hg19: chr1-190745969;