rs62149416

Positions:

• chr2-60856371-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000452343.1(REL-DT):​n.230+403A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,030 control chromosomes in the GnomAD database, including 6,203 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 (6203 hom., cov: 32)
• Consequence: REL-DT ENST00000452343.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989

Genes affected

REL-DT (HGNC:49572): (REL divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
REL-DT	NR_033980.1	n.230+403A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REL-DT	ENST00000439412.6	n.233+403A>G		intron_variant		4
REL-DT	ENST00000452343.1	n.230+403A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39362 AN: 151912 Hom.: 6207 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.259 AC: 39356 AN: 152030 Hom.: 6203 Cov.: 32 AF XY: 0.253 AC XY: 18770 AN XY: 74306

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.274

Alfa AF: 0.316 Hom.: 1833

Bravo AF: 0.248

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62149416; hg19: chr2-61083506;