rs1306395

Positions:

• chr2-60849137-T-C

Variant summary

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

The NR_033980.1(REL-DT):​n.328A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,762 control chromosomes in the GnomAD database, including 11,598 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 0.38 (11584 hom., cov: 30)
  • Exomes 𝑓: 0.44 (14 hom.)
• Consequence: REL-DT NR_033980.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
REL-DT	NR_033980.1	n.328A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REL-DT	ENST00000439412.6	n.234-4911A>G		intron_variant, non_coding_transcript_variant		4
REL-DT	ENST00000452343.1	n.328A>G		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 57949 AN: 151496 Hom.: 11574 Cov.: 30

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.411

GnomAD4 exome AF: 0.439 AC: 65 AN: 148 Hom.: 14 Cov.: 0 AF XY: 0.456 AC XY: 41 AN XY: 90

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.412

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.446

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.382 AC: 57983 AN: 151614 Hom.: 11584 Cov.: 30 AF XY: 0.377 AC XY: 27892 AN XY: 74064

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.406

Alfa AF: 0.422 Hom.: 2800

Bravo AF: 0.381

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1306395; hg19: chr2-61076272;