rs12443973

Variant names:

• chr16-80369399-A-C
• rs12443973
• ENST00000565050.5:n.598+121818T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-80369399-A-C
• chr16-80369399-A-T

Variant summary

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

The ENST00000565050.5(DYNLRB2-AS1):​n.598+121818T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,992 control chromosomes in the GnomAD database, including 38,012 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 0.70 (38012 hom., cov: 31)
• Consequence: DYNLRB2-AS1 ENST00000565050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.747
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+159243T>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNLRB2-AS1	ENST00000565050.5	n.598+121818T>G		intron_variant	Intron 3 of 4	5
DYNLRB2-AS1	ENST00000568776.5	n.252+159243T>G		intron_variant	Intron 2 of 5	4
DYNLRB2-AS1	ENST00000568819.5	n.362+123171T>G		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106255 AN: 151874 Hom.: 37996 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.699 AC: 106304 AN: 151992 Hom.: 38012 Cov.: 31 AF XY: 0.701 AC XY: 52069 AN XY: 74272

African (AFR) AF: 0.536 AC: 22232 AN: 41440

American (AMR) AF: 0.688 AC: 10501 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2693 AN: 3472

East Asian (EAS) AF: 0.795 AC: 4112 AN: 5170

South Asian (SAS) AF: 0.804 AC: 3872 AN: 4818

European-Finnish (FIN) AF: 0.787 AC: 8310 AN: 10554

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.768 AC: 52222 AN: 67958

Other (OTH) AF: 0.709 AC: 1495 AN: 2108

Alfa AF: 0.730 Hom.: 6471

Bravo AF: 0.683

Asia WGS AF: 0.810 AC: 2815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.66
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs12443973; hg19: chr16-80403296;