16-80406404-T-C

Variant names:

• chr16-80406404-T-C
• rs1110789
• ENST00000565050.5:n.598+84813A>G

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+84813A>G variant causes a intron 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 ENST00000565050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 3 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=-0.84).
• 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 rank	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+122238A>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+84813A>G		intron_variant	Intron 3 of 4	5
DYNLRB2-AS1	ENST00000568776.5	n.252+122238A>G		intron_variant	Intron 2 of 5	4
DYNLRB2-AS1	ENST00000568819.5	n.362+86166A>G		intron_variant	Intron 3 of 4	5

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

African (AFR) AF: 0.348 AC: 14416 AN: 41402

American (AMR) AF: 0.354 AC: 5401 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2023 AN: 5158

South Asian (SAS) AF: 0.298 AC: 1434 AN: 4816

European-Finnish (FIN) AF: 0.485 AC: 5124 AN: 10564

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35399 AN: 67944

Other (OTH) AF: 0.447 AC: 942 AN: 2108

Alfa AF: 0.494 Hom.: 68616

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
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1110789; hg19: chr16-80440301;