2-215625044-C-T

Variant names:

• chr2-215625044-C-T
• rs2678272
• ENST00000417485.6:n.284+3119C>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+3119C>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 152,054 control chromosomes in the GnomAD database, including 1,128 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 (1128 hom., cov: 33)
• Consequence: ENSG00000237525 ENST00000417485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 3 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=-0.8).
• 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.724-809G>A		intron	N/A
	LOC102724861	NR_187734.1		n.274+3119C>T		intron	N/A
	LOC102724861	NR_187735.1		n.274+3119C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237525	ENST00000417485.6	TSL:5	n.284+3119C>T		intron	N/A
	ENSG00000237525	ENST00000422353.6	TSL:3	n.288+3119C>T		intron	N/A
	LINC00607	ENST00000423530.5	TSL:2	n.1066-809G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16865 AN: 151936 Hom.: 1125 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.111 AC: 16889 AN: 152054 Hom.: 1128 Cov.: 33 AF XY: 0.115 AC XY: 8512 AN XY: 74284

African (AFR) AF: 0.129 AC: 5334 AN: 41470

American (AMR) AF: 0.111 AC: 1695 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1042 AN: 5186

South Asian (SAS) AF: 0.293 AC: 1408 AN: 4812

European-Finnish (FIN) AF: 0.0619 AC: 653 AN: 10544

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

European-Non Finnish (NFE) AF: 0.0886 AC: 6026 AN: 67982

Other (OTH) AF: 0.102 AC: 215 AN: 2110

Alfa AF: 0.0953 Hom.: 943

Bravo AF: 0.112

Asia WGS AF: 0.252 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2678272; hg19: chr2-216489767;