rs1918172

Variant names:

• chr2-156031988-C-G
• rs1918172
• ENST00000428651.2:n.160-7412G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-156031988-C-G
• chr2-156031988-C-T

Variant summary

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

The ENST00000428651.2(LINC01876):​n.160-7412G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,114 control chromosomes in the GnomAD database, including 52,909 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 0.83 (52909 hom., cov: 32)
• Consequence: LINC01876 ENST00000428651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 17 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.155-7412G>C		intron_variant	Intron 1 of 3
LINC01876	NR_110250.2	n.155-7381G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000428651.2	n.160-7412G>C		intron_variant	Intron 1 of 3	5
LINC01876	ENST00000635799.1	n.153-7412G>C		intron_variant	Intron 1 of 4	5
LINC01876	ENST00000636956.1	n.269-7381G>C		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125470 AN: 151996 Hom.: 52888 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.825 AC: 125541 AN: 152114 Hom.: 52909 Cov.: 32 AF XY: 0.828 AC XY: 61577 AN XY: 74382

African (AFR) AF: 0.637 AC: 26368 AN: 41420

American (AMR) AF: 0.872 AC: 13320 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3054 AN: 3470

East Asian (EAS) AF: 0.804 AC: 4159 AN: 5176

South Asian (SAS) AF: 0.854 AC: 4118 AN: 4824

European-Finnish (FIN) AF: 0.917 AC: 9731 AN: 10614

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61927 AN: 68008

Other (OTH) AF: 0.834 AC: 1764 AN: 2114

Alfa AF: 0.889 Hom.: 33517

Bravo AF: 0.813

Asia WGS AF: 0.818 AC: 2843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.53
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1918172; hg19: chr2-156888500;