rs842639

Variant names:

• chr2-60868110-G-A
• rs842639
• ENST00000439412.6:n.87-11190C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-60868110-G-A
• chr2-60868110-G-C

Variant summary

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

The ENST00000452343.1(REL-DT):​n.84-11190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,052 control chromosomes in the GnomAD database, including 29,453 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 0.61 (29453 hom., cov: 32)
• Consequence: REL-DT ENST00000452343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 28 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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.84-11190C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REL-DT	ENST00000439412.6	TSL:4	n.87-11190C>T		intron	N/A
	REL-DT	ENST00000452343.1	TSL:2	n.84-11190C>T		intron	N/A
	REL-DT	ENST00000748843.1		n.62-11190C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92651 AN: 151936 Hom.: 29420 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.610 AC: 92729 AN: 152052 Hom.: 29453 Cov.: 32 AF XY: 0.602 AC XY: 44716 AN XY: 74314

African (AFR) AF: 0.595 AC: 24692 AN: 41468

American (AMR) AF: 0.531 AC: 8109 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2764 AN: 3472

East Asian (EAS) AF: 0.132 AC: 683 AN: 5180

South Asian (SAS) AF: 0.336 AC: 1617 AN: 4816

European-Finnish (FIN) AF: 0.660 AC: 6969 AN: 10558

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45725 AN: 67968

Other (OTH) AF: 0.651 AC: 1375 AN: 2112

Alfa AF: 0.657 Hom.: 52901

Bravo AF: 0.601

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.75
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs842639; hg19: chr2-61095245;