2-60854407-C-T

Variant names:

• chr2-60854407-C-T
• rs702873
• ENST00000439412.6:n.233+2367G>A

Variant summary

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

The ENST00000439412.6(REL-DT):​n.233+2367G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,962 control chromosomes in the GnomAD database, including 10,260 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 (10260 hom., cov: 31)
• Consequence: REL-DT ENST00000439412.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 61 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 = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
REL-DT	NR_033980.1	n.230+2367G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
REL-DT	ENST00000439412.6	n.233+2367G>A		intron_variant	Intron 2 of 3	4
REL-DT	ENST00000452343.1	n.230+2367G>A		intron_variant	Intron 2 of 2	2
REL-DT	ENST00000748843.1	n.193+2382G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53543 AN: 151846 Hom.: 10262 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.352 AC: 53550 AN: 151962 Hom.: 10260 Cov.: 31 AF XY: 0.348 AC XY: 25845 AN XY: 74240

African (AFR) AF: 0.241 AC: 9971 AN: 41444

American (AMR) AF: 0.340 AC: 5196 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3470

East Asian (EAS) AF: 0.123 AC: 638 AN: 5182

South Asian (SAS) AF: 0.208 AC: 1001 AN: 4816

European-Finnish (FIN) AF: 0.401 AC: 4219 AN: 10530

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29734 AN: 67946

Other (OTH) AF: 0.383 AC: 809 AN: 2110

Alfa AF: 0.403 Hom.: 44295

Bravo AF: 0.347

Asia WGS AF: 0.157 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.80
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs702873; hg19: chr2-61081542;