chr13-50878615-T-C

Variant names:

• chr13-50878615-T-C
• rs2408213
• ENST00000660528.1:n.2464A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660528.1(RNASEH2B-AS1):​n.2464A>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 0.306 in 152,056 control chromosomes in the GnomAD database, including 7,708 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 0.31 (7708 hom., cov: 31)
• Consequence: RNASEH2B-AS1 ENST00000660528.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 3 publications found

Genes affected

RNASEH2B-AS1 (HGNC:39967): (RNASEH2B antisense RNA 1)

DLEU1 (HGNC:13747): (deleted in lymphocytic leukemia 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNASEH2B-AS1	ENST00000660528.1	n.2464A>G		non_coding_transcript_exon_variant	Exon 3 of 3
RNASEH2B-AS1	ENST00000596992.5	n.518-1653A>G		intron_variant	Intron 4 of 4	5
RNASEH2B-AS1	ENST00000631080.2	n.433+3896A>G		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46539 AN: 151938 Hom.: 7695 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.306 AC: 46597 AN: 152056 Hom.: 7708 Cov.: 31 AF XY: 0.303 AC XY: 22556 AN XY: 74324

African (AFR) AF: 0.426 AC: 17673 AN: 41452

American (AMR) AF: 0.268 AC: 4095 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3470

East Asian (EAS) AF: 0.404 AC: 2092 AN: 5172

South Asian (SAS) AF: 0.235 AC: 1132 AN: 4820

European-Finnish (FIN) AF: 0.222 AC: 2347 AN: 10572

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17337 AN: 67990

Other (OTH) AF: 0.300 AC: 632 AN: 2106

Alfa AF: 0.268 Hom.: 9468

Bravo AF: 0.318

Asia WGS AF: 0.309 AC: 1076 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.8
DANN	Benign	0.82
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2408213; hg19: chr13-51452751;