rs842634

Variant names:

• chr2-60864087-T-C
• rs842634
• ENST00000439412.6:n.87-7167A>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.84-7167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 151,604 control chromosomes in the GnomAD database, including 45,213 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 0.76 (45213 hom., cov: 27)
• Consequence: REL-DT ENST00000452343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 12 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 (AFR) allele frequency at 95% confidence interval = 0.927 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.84-7167A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REL-DT	ENST00000439412.6	TSL:4	n.87-7167A>G		intron	N/A
	REL-DT	ENST00000452343.1	TSL:2	n.84-7167A>G		intron	N/A
	REL-DT	ENST00000748843.1		n.62-7167A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115291 AN: 151486 Hom.: 45160 Cov.: 27

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.761 AC: 115393 AN: 151604 Hom.: 45213 Cov.: 27 AF XY: 0.754 AC XY: 55828 AN XY: 74036

African (AFR) AF: 0.935 AC: 38650 AN: 41358

American (AMR) AF: 0.689 AC: 10485 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2876 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2824 AN: 5136

South Asian (SAS) AF: 0.389 AC: 1862 AN: 4784

European-Finnish (FIN) AF: 0.706 AC: 7387 AN: 10464

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48812 AN: 67872

Other (OTH) AF: 0.782 AC: 1647 AN: 2106

Alfa AF: 0.740 Hom.: 107833

Bravo AF: 0.771

Asia WGS AF: 0.484 AC: 1683 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	2.6
DANN	Benign	0.66
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs842634; hg19: chr2-61091222;