chr2-15786044-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905976	XR_007086225.1	n.1147T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01804	ENST00000770646.1	n.1463T>C		non_coding_transcript_exon_variant	Exon 5 of 5
LINC01804	ENST00000770654.1	n.1322T>C		non_coding_transcript_exon_variant	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 v4.3

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

Other links and lift over

dbSNP: rs2544527; hg19: chr2-15926168;