chr2-14038859-A-G

Variant names:

• chr2-14038859-A-G
• rs9287767
• ENST00000417751.5:n.257-197245T>C

Variant summary

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

The ENST00000417751.5(LINC00276):​n.257-197245T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,190 control chromosomes in the GnomAD database, including 4,538 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 0.15 (4538 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 1 publications found

Genes affected

LINC00276 (HGNC:38663): (long intergenic non-protein coding RNA 276)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417751.5. 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
	LINC00276	ENST00000417751.5	TSL:2	n.257-197245T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22474 AN: 152072 Hom.: 4510 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.00820

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.00882

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.148 AC: 22550 AN: 152190 Hom.: 4538 Cov.: 32 AF XY: 0.146 AC XY: 10890 AN XY: 74426

African (AFR) AF: 0.449 AC: 18600 AN: 41460

American (AMR) AF: 0.0668 AC: 1022 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0855 AC: 297 AN: 3472

East Asian (EAS) AF: 0.209 AC: 1081 AN: 5172

South Asian (SAS) AF: 0.118 AC: 568 AN: 4822

European-Finnish (FIN) AF: 0.00820 AC: 87 AN: 10616

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.00880 AC: 599 AN: 68034

Other (OTH) AF: 0.121 AC: 256 AN: 2112

Alfa AF: 0.0532 Hom.: 637

Bravo AF: 0.166

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		-0.16

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: rs9287767;

hg19: chr2-14178984;