rs4581712

Positions:

• chr16-80463704-C-A

Variant summary

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

The NR_120307.1(DYNLRB2-AS1):​n.252+64938G>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 0.226 in 152,072 control chromosomes in the GnomAD database, including 4,594 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 0.23 (4594 hom., cov: 32)
• Consequence: DYNLRB2-AS1 NR_120307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+64938G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNLRB2-AS1	ENST00000668341.1	n.417+64938G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34426 AN: 151954 Hom.: 4596 Cov.: 32

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.226 AC: 34420 AN: 152072 Hom.: 4594 Cov.: 32 AF XY: 0.231 AC XY: 17195 AN XY: 74326

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.256

Alfa AF: 0.263 Hom.: 5693

Bravo AF: 0.215

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4581712; hg19: chr16-80497601;