1-121430980-T-G

Position:

• chr1-121430980-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417218.1(LINC02798):​n.552-29039T>G variant causes a intron, non coding transcript 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 ENST00000417218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02798	XM_047438024.1	c.*378-29039T>G		intron_variant
LINC02798	XR_007066532.1	n.825+2916T>G		intron_variant, non_coding_transcript_variant
LINC02798	XR_007066534.1	n.550-29039T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02798	ENST00000668551.1	n.320-29039T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.530

Alfa AF: 0.513 Hom.: 5335

Bravo AF: 0.499

Asia WGS AF: 0.469 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7532615; hg19: chr1-121172840; COSMIC: COSV69885485;