rs1125733

Positions:

• chr16-80418343-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_120307.1(DYNLRB2-AS1):​n.252+110299T>C variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.332 in 149,034 control chromosomes in the GnomAD database, including 9,800 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 0.33 (9800 hom., cov: 32)
• Consequence: DYNLRB2-AS1 NR_120307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.64

Genes affected

DYNLRB2-AS1 (HGNC:55405): (DYNLRB2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+110299T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DYNLRB2-AS1	ENST00000668341.1	n.417+110299T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.332 AC: 49513 AN: 148914 Hom.: 9804 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.441

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.332 AC: 49512 AN: 149034 Hom.: 9800 Cov.: 32 AF XY: 0.330 AC XY: 24070 AN XY: 72888

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.360

Alfa AF: 0.422 Hom.: 13218

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	18
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: rs1125733; hg19: chr16-80452240;