chr2-60849137-T-C

Variant names:

• chr2-60849137-T-C
• rs1306395
• ENST00000452343.1:n.328A>G

Variant summary

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

The ENST00000452343.1(REL-DT):​n.328A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,762 control chromosomes in the GnomAD database, including 11,598 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 0.38 (11584 hom., cov: 30)
  • Exomes 𝑓: 0.44 (14 hom.)
• Consequence: REL-DT ENST00000452343.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07
• Publications: 8 publications found

Genes affected

REL-DT (HGNC:49572): (REL divergent transcript)

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 = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452343.1. 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
	REL-DT	NR_033980.1		n.328A>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REL-DT	ENST00000452343.1	TSL:2	n.328A>G		non_coding_transcript_exon	Exon 3 of 3
	REL-DT	ENST00000439412.6	TSL:4	n.234-4911A>G		intron	N/A
	REL-DT	ENST00000748843.1		n.194-4911A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 57949 AN: 151496 Hom.: 11574 Cov.: 30

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.411

GnomAD4 exome AF: 0.439 AC: 65 AN: 148 Hom.: 14 Cov.: 0 AF XY: 0.456 AC XY: 41 AN XY: 90

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.412 AC: 33 AN: 80

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.446 AC: 25 AN: 56

Other (OTH) AF: 0.500 AC: 3 AN: 6

GnomAD4 genome AF: 0.382 AC: 57983 AN: 151614 Hom.: 11584 Cov.: 30 AF XY: 0.377 AC XY: 27892 AN XY: 74064

African (AFR) AF: 0.343 AC: 14191 AN: 41328

American (AMR) AF: 0.351 AC: 5346 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3472

East Asian (EAS) AF: 0.126 AC: 650 AN: 5166

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4810

European-Finnish (FIN) AF: 0.400 AC: 4181 AN: 10464

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29731 AN: 67856

Other (OTH) AF: 0.406 AC: 852 AN: 2100

Alfa AF: 0.420 Hom.: 2846

Bravo AF: 0.381

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.38
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs1306395; hg19: chr2-61076272; COSMIC: COSV107526424;