2-60854407-C-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.230+2367G>A 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 0.352 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 NR_033980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

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=-0.88).
• 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/exons	MANE	UniProt
REL-DT	NR_033980.1	n.230+2367G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REL-DT	ENST00000439412.6	n.233+2367G>A		intron_variant, non_coding_transcript_variant		4
REL-DT	ENST00000452343.1	n.230+2367G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.383

Alfa AF: 0.409 Hom.: 20166

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs702873; hg19: chr2-61081542;