rs8060581

Variant names:

• chr16-80158708-G-C
• rs8060581
• ENST00000563397.1:n.393-8696G>C

Variant summary

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

The ENST00000563397.1(ENSG00000260706):​n.393-8696G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,120 control chromosomes in the GnomAD database, including 3,561 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 0.16 (3561 hom., cov: 32)
• Consequence: ENSG00000260706 ENST00000563397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 4 publications found

Genes affected

ENSG00000260706 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.446+629C>G		intron_variant	Intron 4 of 5
LOC105371357	XR_933774.3	n.393-8696G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260706	ENST00000563397.1	n.393-8696G>C		intron_variant	Intron 2 of 2	4
DYNLRB2-AS1	ENST00000565050.5	n.717+629C>G		intron_variant	Intron 4 of 4	5
DYNLRB2-AS1	ENST00000568776.5	n.446+629C>G		intron_variant	Intron 4 of 5	4

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24050 AN: 152002 Hom.: 3538 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.159 AC: 24122 AN: 152120 Hom.: 3561 Cov.: 32 AF XY: 0.159 AC XY: 11853 AN XY: 74374

African (AFR) AF: 0.389 AC: 16119 AN: 41450

American (AMR) AF: 0.106 AC: 1615 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1077 AN: 5180

South Asian (SAS) AF: 0.171 AC: 821 AN: 4812

European-Finnish (FIN) AF: 0.0501 AC: 531 AN: 10590

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0498 AC: 3388 AN: 68004

Other (OTH) AF: 0.134 AC: 284 AN: 2114

Alfa AF: 0.115 Hom.: 275

Bravo AF: 0.171

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs8060581; hg19: chr16-80192605;