rs1609516

Positions:

• chr16-80251987-A-G

Variant summary

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

The NR_120307.1(DYNLRB2-AS1):​n.253-91681T>C 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 0.611 in 152,068 control chromosomes in the GnomAD database, including 28,602 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 0.61 (28602 hom., cov: 33)
• Consequence: DYNLRB2-AS1 NR_120307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.253-91681T>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.418-91666T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92893 AN: 151950 Hom.: 28576 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.611 AC: 92962 AN: 152068 Hom.: 28602 Cov.: 33 AF XY: 0.607 AC XY: 45140 AN XY: 74336

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.612

Alfa AF: 0.611 Hom.: 8983

Bravo AF: 0.614

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.29
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1609516; hg19: chr16-80285884;