1-121430980-T-G

Variant names:

• chr1-121430980-T-G
• rs7532615
• ENST00000417218.2:n.1066-29039T>G

Variant summary

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

The ENST00000417218.2(LINC02798):​n.1066-29039T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,076 control chromosomes in the GnomAD database, including 20,775 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 0.51 (20775 hom., cov: 32)
• Consequence: LINC02798 ENST00000417218.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 14 publications found

Genes affected

LINC02798 (HGNC:54323): (long intergenic non-protein coding RNA 2798)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417218.2. 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
	LINC02798	ENST00000417218.2	TSL:1	n.1066-29039T>G		intron	N/A
	LINC02798	ENST00000650414.1		n.595+2916T>G		intron	N/A
	LINC02798	ENST00000664311.1		n.330-29039T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77194 AN: 151958 Hom.: 20768 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.508 AC: 77234 AN: 152076 Hom.: 20775 Cov.: 32 AF XY: 0.509 AC XY: 37832 AN XY: 74330

African (AFR) AF: 0.313 AC: 12983 AN: 41466

American (AMR) AF: 0.533 AC: 8148 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1826 AN: 3472

East Asian (EAS) AF: 0.629 AC: 3258 AN: 5178

South Asian (SAS) AF: 0.401 AC: 1931 AN: 4820

European-Finnish (FIN) AF: 0.644 AC: 6797 AN: 10562

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40560 AN: 67982

Other (OTH) AF: 0.530 AC: 1119 AN: 2112

Alfa AF: 0.539 Hom.: 10124

Bravo AF: 0.499

Asia WGS AF: 0.469 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.5
DANN	Benign	0.90
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7532615;

hg19: chr1-121172840;

COSMIC: COSV69885485;