chr2-15753767-G-T

Variant names:

• chr2-15753767-G-T
• rs6705499
• ENST00000770646.1:n.529-29380G>T

Variant summary

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

The ENST00000770646.1(LINC01804):​n.529-29380G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,976 control chromosomes in the GnomAD database, including 10,780 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 0.36 (10780 hom., cov: 31)
• Consequence: LINC01804 ENST00000770646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 3 publications found

Genes affected

LINC01804 (HGNC:52596): (long intergenic non-protein coding RNA 1804)

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 (AMR) allele frequency at 95% confidence interval = 0.449 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
LINC01804	ENST00000770646.1	n.529-29380G>T		intron_variant	Intron 3 of 4
LINC01804	ENST00000770647.1	n.407-29380G>T		intron_variant	Intron 2 of 3
LINC01804	ENST00000770648.1	n.430-27837G>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55247 AN: 151858 Hom.: 10773 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.364 AC: 55299 AN: 151976 Hom.: 10780 Cov.: 31 AF XY: 0.364 AC XY: 27020 AN XY: 74244

African (AFR) AF: 0.215 AC: 8934 AN: 41484

American (AMR) AF: 0.458 AC: 7002 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3464

East Asian (EAS) AF: 0.330 AC: 1701 AN: 5148

South Asian (SAS) AF: 0.298 AC: 1428 AN: 4796

European-Finnish (FIN) AF: 0.409 AC: 4303 AN: 10532

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28964 AN: 67950

Other (OTH) AF: 0.404 AC: 855 AN: 2114

Alfa AF: 0.407 Hom.: 54728

Bravo AF: 0.363

Asia WGS AF: 0.297 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.082
DANN	Benign	0.50
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6705499; hg19: chr2-15893891;