chr2-60864815-G-A

Variant names:

• chr2-60864815-G-A
• rs842636
• ENST00000439412.6:n.87-7895C>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.84-7895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,844 control chromosomes in the GnomAD database, including 12,137 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 0.39 (12137 hom., cov: 31)
• Consequence: REL-DT ENST00000452343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 25 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=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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.84-7895C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REL-DT	ENST00000439412.6	TSL:4	n.87-7895C>T		intron	N/A
	REL-DT	ENST00000452343.1	TSL:2	n.84-7895C>T		intron	N/A
	REL-DT	ENST00000748843.1		n.62-7895C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59403 AN: 151728 Hom.: 12127 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.391 AC: 59439 AN: 151844 Hom.: 12137 Cov.: 31 AF XY: 0.386 AC XY: 28602 AN XY: 74180

African (AFR) AF: 0.356 AC: 14745 AN: 41372

American (AMR) AF: 0.362 AC: 5519 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1652 AN: 3466

East Asian (EAS) AF: 0.123 AC: 636 AN: 5176

South Asian (SAS) AF: 0.223 AC: 1070 AN: 4808

European-Finnish (FIN) AF: 0.404 AC: 4257 AN: 10528

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30242 AN: 67938

Other (OTH) AF: 0.414 AC: 870 AN: 2102

Alfa AF: 0.422 Hom.: 43052

Bravo AF: 0.390

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.9
DANN	Benign	0.84
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs842636; hg19: chr2-61091950;