rs11859036

Variant names:

• chr16-80271654-C-A
• rs11859036
• ENST00000565050.5:n.599-112199G>T

Your query was ambiguous. Multiple possible variants found:

• chr16-80271654-C-A
• chr16-80271654-C-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.599-112199G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,036 control chromosomes in the GnomAD database, including 7,614 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 0.30 (7614 hom., cov: 32)
• Consequence: DYNLRB2-AS1 ENST00000565050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.253-111348G>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNLRB2-AS1	ENST00000565050.5	n.599-112199G>T		intron_variant	Intron 3 of 4	5
DYNLRB2-AS1	ENST00000568776.5	n.253-111348G>T		intron_variant	Intron 2 of 5	4
DYNLRB2-AS1	ENST00000568819.5	n.363-52788G>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45595 AN: 151920 Hom.: 7613 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.300 AC: 45607 AN: 152036 Hom.: 7614 Cov.: 32 AF XY: 0.290 AC XY: 21559 AN XY: 74312

African (AFR) AF: 0.224 AC: 9287 AN: 41476

American (AMR) AF: 0.238 AC: 3628 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3470

East Asian (EAS) AF: 0.0152 AC: 79 AN: 5182

South Asian (SAS) AF: 0.144 AC: 692 AN: 4820

European-Finnish (FIN) AF: 0.292 AC: 3080 AN: 10540

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26708 AN: 67968

Other (OTH) AF: 0.302 AC: 637 AN: 2110

Alfa AF: 0.351 Hom.: 41524

Bravo AF: 0.292

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.80
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs11859036; hg19: chr16-80305551;