rs842636

chr2-60864815-G-A

Variant summary

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

The NR_033980.1(REL-DT):n.84-7895C>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 0.391 in 151,844 control chromosomes in the GnomAD database, including 12,137 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 0.39 (12137 hom., cov: 31)
• Consequence: REL-DT NR_033980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651

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=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
REL-DT	NR_033980.1	n.84-7895C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REL-DT	ENST00000439412.6	n.87-7895C>T		intron_variant, non_coding_transcript_variant		4
REL-DT	ENST00000452343.1	n.84-7895C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59403 AN: 151728 Hom.: 12127 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.391 AC: 59439 AN: 151844 Hom.: 12137 Cov.: 31 AF XY: 0.386 AC XY: 28602 AN XY: 74180

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.414

Alfa AF: 0.428 Hom.: 17124

Bravo AF: 0.390

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	7.9
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs842636; hg19: chr2-61091950;