rs4664789

Variant names:

• chr2-156011024-C-A
• rs4664789
• ENST00000637476.2:n.1550G>T

Variant summary

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

The ENST00000637476.2(LINC01876):​n.1550G>T 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 0.459 in 151,924 control chromosomes in the GnomAD database, including 16,299 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 0.46 (16299 hom., cov: 32)
• Consequence: LINC01876 ENST00000637476.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647
• Publications: 4 publications found

Genes affected

LINC01876 (HGNC:52695): (long intergenic non-protein coding RNA 1876)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.527 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
LINC01876	ENST00000637476.2	n.1550G>T		non_coding_transcript_exon_variant	Exon 7 of 7	4
LINC01876	ENST00000824378.1	n.1664G>T		non_coding_transcript_exon_variant	Exon 7 of 7

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69679 AN: 151806 Hom.: 16284 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.459 AC: 69719 AN: 151924 Hom.: 16299 Cov.: 32 AF XY: 0.456 AC XY: 33840 AN XY: 74244

African (AFR) AF: 0.371 AC: 15383 AN: 41424

American (AMR) AF: 0.536 AC: 8204 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3466

East Asian (EAS) AF: 0.448 AC: 2309 AN: 5158

South Asian (SAS) AF: 0.413 AC: 1991 AN: 4818

European-Finnish (FIN) AF: 0.399 AC: 4197 AN: 10522

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34275 AN: 67934

Other (OTH) AF: 0.472 AC: 994 AN: 2106

Alfa AF: 0.491 Hom.: 9513

Bravo AF: 0.468

Asia WGS AF: 0.407 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.3
DANN	Benign	0.41
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs4664789; hg19: chr2-156867536;