chr2-60855525-G-A

Variant names:

• chr2-60855525-G-A
• rs842627
• ENST00000439412.6:n.233+1249C>T

Variant summary

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

The ENST00000452343.1(REL-DT):​n.230+1249C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,034 control chromosomes in the GnomAD database, including 10,256 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 0.35 (10256 hom., cov: 29)
• Consequence: REL-DT ENST00000452343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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.230+1249C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REL-DT	ENST00000439412.6	TSL:4	n.233+1249C>T		intron	N/A
	REL-DT	ENST00000452343.1	TSL:2	n.230+1249C>T		intron	N/A
	REL-DT	ENST00000748843.1		n.193+1264C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53382 AN: 150920 Hom.: 10257 Cov.: 29

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.353 AC: 53389 AN: 151034 Hom.: 10256 Cov.: 29 AF XY: 0.349 AC XY: 25741 AN XY: 73712

African (AFR) AF: 0.241 AC: 9892 AN: 41096

American (AMR) AF: 0.341 AC: 5175 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1541 AN: 3466

East Asian (EAS) AF: 0.124 AC: 633 AN: 5100

South Asian (SAS) AF: 0.208 AC: 992 AN: 4780

European-Finnish (FIN) AF: 0.400 AC: 4153 AN: 10372

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.439 AC: 29756 AN: 67758

Other (OTH) AF: 0.381 AC: 795 AN: 2084

Alfa AF: 0.398 Hom.: 1600

Bravo AF: 0.347

Asia WGS AF: 0.157 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs842627; hg19: chr2-61082660;