2-15786044-T-C

Variant names:

• chr2-15786044-T-C
• rs2544527
• ENST00000770646.1:n.1463T>C

Variant summary

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

The ENST00000770646.1(LINC01804):​n.1463T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,122 control chromosomes in the GnomAD database, including 46,544 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 0.77 (46544 hom., cov: 32)
• Consequence: LINC01804 ENST00000770646.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 10 publications found

Genes affected

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

LOC124905976 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770646.1. 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
	LINC01804	ENST00000770646.1		n.1463T>C		non_coding_transcript_exon	Exon 5 of 5
	LINC01804	ENST00000770654.1		n.1322T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117478 AN: 152004 Hom.: 46480 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.773 AC: 117601 AN: 152122 Hom.: 46544 Cov.: 32 AF XY: 0.774 AC XY: 57566 AN XY: 74328

African (AFR) AF: 0.944 AC: 39205 AN: 41528

American (AMR) AF: 0.802 AC: 12257 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2462 AN: 3468

East Asian (EAS) AF: 0.772 AC: 3970 AN: 5144

South Asian (SAS) AF: 0.709 AC: 3414 AN: 4816

European-Finnish (FIN) AF: 0.734 AC: 7764 AN: 10580

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46227 AN: 67990

Other (OTH) AF: 0.763 AC: 1611 AN: 2112

Alfa AF: 0.713 Hom.: 154511

Bravo AF: 0.786

Asia WGS AF: 0.764 AC: 2660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.62
PhyloP100		-1.1

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: rs2544527;

hg19: chr2-15926168;