rs1609516

Variant names:

• chr16-80251987-A-G
• rs1609516
• ENST00000565050.5:n.599-92532T>C

Variant summary

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

The ENST00000568776.5(DYNLRB2-AS1):​n.253-91681T>C variant causes a intron 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 ENST00000568776.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568776.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2-AS1	NR_120307.1		n.253-91681T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2-AS1	ENST00000565050.5	TSL:5	n.599-92532T>C		intron	N/A
	DYNLRB2-AS1	ENST00000568776.5	TSL:4	n.253-91681T>C		intron	N/A
	DYNLRB2-AS1	ENST00000568819.5	TSL:5	n.363-33121T>C		intron	N/A

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

African (AFR) AF: 0.652 AC: 27018 AN: 41452

American (AMR) AF: 0.584 AC: 8927 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2096 AN: 3466

East Asian (EAS) AF: 0.462 AC: 2386 AN: 5168

South Asian (SAS) AF: 0.472 AC: 2279 AN: 4826

European-Finnish (FIN) AF: 0.623 AC: 6583 AN: 10574

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41602 AN: 67978

Other (OTH) AF: 0.612 AC: 1292 AN: 2110

Alfa AF: 0.612 Hom.: 13362

Bravo AF: 0.614

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.29
DANN	Benign	0.76
PhyloP100		-0.43

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1609516;

hg19: chr16-80285884;