rs1432295

chr2-60839531-G-Achr2-60839531-G-Cchr2-60839531-G-T

Variant summary

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

The ENST00000439412.6(REL-DT):n.403+4526C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,056 control chromosomes in the GnomAD database, including 37,430 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 0.69 (37430 hom., cov: 31)
• Consequence: REL-DT ENST00000439412.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REL-DT	ENST00000439412.6	n.403+4526C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104876 AN: 151938 Hom.: 37375 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.690 AC: 104991 AN: 152056 Hom.: 37430 Cov.: 31 AF XY: 0.695 AC XY: 51620 AN XY: 74314

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.665

Alfa AF: 0.626 Hom.: 66413

Bravo AF: 0.705

Asia WGS AF: 0.920 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.88
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1432295; hg19: chr2-61066666;