rs2680182

Variant names:

• chr2-215625359-C-T
• rs2680182
• ENST00000417485.6:n.284+3434C>T

Variant summary

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

The ENST00000417485.6(ENSG00000237525):​n.284+3434C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,170 control chromosomes in the GnomAD database, including 1,126 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 0.11 (1126 hom., cov: 33)
• Consequence: ENSG00000237525 ENST00000417485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 4 publications found

Genes affected

ENSG00000237525 (HGNC:):

LINC00607 (HGNC:43944): (long intergenic non-protein coding RNA 607)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417485.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00607	NR_037195.1		n.724-1124G>A		intron	N/A
	LOC102724861	NR_187734.1		n.274+3434C>T		intron	N/A
	LOC102724861	NR_187735.1		n.274+3434C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237525	ENST00000417485.6	TSL:5	n.284+3434C>T		intron	N/A
	ENSG00000237525	ENST00000422353.6	TSL:3	n.288+3434C>T		intron	N/A
	LINC00607	ENST00000423530.5	TSL:2	n.1066-1124G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16858 AN: 152052 Hom.: 1123 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.0620

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.111 AC: 16882 AN: 152170 Hom.: 1126 Cov.: 33 AF XY: 0.114 AC XY: 8516 AN XY: 74410

African (AFR) AF: 0.129 AC: 5336 AN: 41498

American (AMR) AF: 0.110 AC: 1683 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1037 AN: 5180

South Asian (SAS) AF: 0.293 AC: 1414 AN: 4824

European-Finnish (FIN) AF: 0.0620 AC: 657 AN: 10596

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0886 AC: 6025 AN: 67996

Other (OTH) AF: 0.101 AC: 213 AN: 2116

Alfa AF: 0.107 Hom.: 591

Bravo AF: 0.112

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.34
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2680182; hg19: chr2-216490082;