2-60879336-A-G

Variant names:

• chr2-60879336-A-G
• rs13031721
• ENST00000439412.6:n.86+1896T>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.83+1896T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,114 control chromosomes in the GnomAD database, including 6,256 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 0.26 (6256 hom., cov: 32)
• Consequence: REL-DT ENST00000452343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 7 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 = 0.367 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.83+1896T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REL-DT	ENST00000439412.6	TSL:4	n.86+1896T>C		intron	N/A
	REL-DT	ENST00000452343.1	TSL:2	n.83+1896T>C		intron	N/A
	REL-DT	ENST00000748843.1		n.61+1896T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38920 AN: 151996 Hom.: 6258 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.256 AC: 38920 AN: 152114 Hom.: 6256 Cov.: 32 AF XY: 0.249 AC XY: 18537 AN XY: 74362

African (AFR) AF: 0.0969 AC: 4024 AN: 41536

American (AMR) AF: 0.237 AC: 3614 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3470

East Asian (EAS) AF: 0.0179 AC: 93 AN: 5190

South Asian (SAS) AF: 0.0867 AC: 418 AN: 4822

European-Finnish (FIN) AF: 0.341 AC: 3590 AN: 10534

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25196 AN: 67972

Other (OTH) AF: 0.276 AC: 582 AN: 2108

Alfa AF: 0.309 Hom.: 996

Bravo AF: 0.244

Asia WGS AF: 0.0590 AC: 205 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.45
PhyloP100		-0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13031721;

hg19: chr2-61106471;