chr2-101975535-T-C

Variant names:

• chr2-101975535-T-C
• rs12712122
• ENST00000627215.2:n.274-8157T>C

Variant summary

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

The ENST00000627215.2(LINC01127):​n.274-8157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 151,906 control chromosomes in the GnomAD database, including 40,326 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 0.72 (40326 hom., cov: 29)
• Consequence: LINC01127 ENST00000627215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.85
• Publications: 9 publications found

Genes affected

LINC01127 (HGNC:49292): (long intergenic non-protein coding RNA 1127)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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
LINC01127	ENST00000627215.2	n.274-8157T>C		intron_variant	Intron 2 of 2	2
LINC01127	ENST00000627273.3	n.256-8157T>C		intron_variant	Intron 2 of 4	4
LINC01127	ENST00000628502.3	n.248-236T>C		intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109815 AN: 151788 Hom.: 40282 Cov.: 29

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.724 AC: 109909 AN: 151906 Hom.: 40326 Cov.: 29 AF XY: 0.730 AC XY: 54218 AN XY: 74222

African (AFR) AF: 0.785 AC: 32504 AN: 41428

American (AMR) AF: 0.726 AC: 11098 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2132 AN: 3468

East Asian (EAS) AF: 0.973 AC: 5003 AN: 5142

South Asian (SAS) AF: 0.722 AC: 3471 AN: 4808

European-Finnish (FIN) AF: 0.815 AC: 8597 AN: 10552

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44897 AN: 67920

Other (OTH) AF: 0.706 AC: 1487 AN: 2106

Alfa AF: 0.712 Hom.: 5007

Bravo AF: 0.723

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.022
DANN	Benign	0.11
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs12712122; hg19: chr2-102591997;