rs1073981

Variant names:

• chr2-66782579-G-A
• rs1073981
• ENST00000715601.1:n.185-65407G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-66782579-G-A
• chr2-66782579-G-T

Variant summary

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

The ENST00000715601.1(LINC01798):​n.185-65407G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.035 in 152,186 control chromosomes in the GnomAD database, including 226 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 0.035 (226 hom., cov: 32)
• Consequence: LINC01798 ENST00000715601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 2 publications found

Genes affected

LINC01798 (HGNC:52588): (long intergenic non-protein coding RNA 1798)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.117 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
LINC01798	ENST00000715601.1	n.185-65407G>A		intron_variant	Intron 2 of 6
LINC01798	ENST00000758432.1	n.185-65407G>A		intron_variant	Intron 2 of 5
LINC01798	ENST00000758436.1	n.247-65407G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0350 AC: 5316 AN: 152068 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.00780

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0941

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0808

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0350 AC: 5329 AN: 152186 Hom.: 226 Cov.: 32 AF XY: 0.0404 AC XY: 3004 AN XY: 74390

African (AFR) AF: 0.00782 AC: 325 AN: 41540

American (AMR) AF: 0.0946 AC: 1445 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3472

East Asian (EAS) AF: 0.125 AC: 646 AN: 5178

South Asian (SAS) AF: 0.0952 AC: 458 AN: 4812

European-Finnish (FIN) AF: 0.0808 AC: 855 AN: 10580

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0207 AC: 1406 AN: 68010

Other (OTH) AF: 0.0398 AC: 84 AN: 2110

Alfa AF: 0.0112 Hom.: 5

Bravo AF: 0.0358

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.74
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs1073981; hg19: chr2-67009711;