16-80406404-T-C

Position:

• chr16-80406404-T-C

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+122238A>G 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 0.439 in 151,928 control chromosomes in the GnomAD database, including 15,301 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 0.44 (15301 hom., cov: 31)
• Consequence: DYNLRB2-AS1 NR_120307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+122238A>G		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+122238A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66703 AN: 151810 Hom.: 15286 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.439 AC: 66755 AN: 151928 Hom.: 15301 Cov.: 31 AF XY: 0.435 AC XY: 32318 AN XY: 74276

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.447

Alfa AF: 0.499 Hom.: 29776

Bravo AF: 0.423

Asia WGS AF: 0.332 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1110789; hg19: chr16-80440301;