rs6600671

Positions:

• chr1-121458637-G-T

Variant summary

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

The ENST00000417218.1(LINC02798):​n.552-1382G>T 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 0.624 in 151,964 control chromosomes in the GnomAD database, including 29,694 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 0.62 (29694 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02798	XM_047438024.1	c.*378-1382G>T		intron_variant			XP_047293980.1
LINC02798	XR_007066532.1	n.826-1382G>T		intron_variant, non_coding_transcript_variant
LINC02798	XR_007066534.1	n.550-1382G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02798	ENST00000668551.1	n.320-1382G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94689 AN: 151846 Hom.: 29663 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.624 AC: 94786 AN: 151964 Hom.: 29694 Cov.: 32 AF XY: 0.626 AC XY: 46460 AN XY: 74250

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.620

Alfa AF: 0.611 Hom.: 27038

Bravo AF: 0.631

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6600671; hg19: chr1-121200490;