rs11859036

Positions:

• chr16-80271654-C-A
• chr16-80271654-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120307.1(DYNLRB2-AS1):​n.253-111348G>T variant causes a intron, non coding transcript 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 NR_120307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DYNLRB2-AS1	NR_120307.1	n.253-111348G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNLRB2-AS1	ENST00000668341.1	n.418-111333G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.0152

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.302

Alfa AF: 0.356 Hom.: 18770

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11859036; hg19: chr16-80305551;