rs13031721

Positions:

• chr2-60879336-A-G
• chr2-60879336-A-T

Variant summary

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

The NR_033980.1(REL-DT):​n.83+1896T>C 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 0.256 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 NR_033980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

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 = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
REL-DT	NR_033980.1	n.83+1896T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REL-DT	ENST00000439412.6	n.86+1896T>C		intron_variant, non_coding_transcript_variant		4
REL-DT	ENST00000452343.1	n.83+1896T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0179

Gnomad4 SAS AF: 0.0867

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.276

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13031721; hg19: chr2-61106471;