rs10514490

chr16-80217368-G-Achr16-80217368-G-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.253-57062C>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 0.0394 in 152,214 control chromosomes in the GnomAD database, including 291 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 0.039 (291 hom., cov: 33)
• Consequence: DYNLRB2-AS1 NR_120307.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

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 (EAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNLRB2-AS1	NR_120307.1	n.253-57062C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DYNLRB2-AS1	ENST00000668341.1	n.418-57047C>T		intron_variant, non_coding_transcript_variant
DYNLRB2-AS1	ENST00000565050.5	n.599-57913C>T		intron_variant, non_coding_transcript_variant		5
DYNLRB2-AS1	ENST00000568776.5	n.253-57062C>T		intron_variant, non_coding_transcript_variant		4
DYNLRB2-AS1	ENST00000666474.1	n.646-57047C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 5989 AN: 152096 Hom.: 288 Cov.: 33

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0485

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.00490

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00715

Gnomad OTH AF: 0.0412

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

GnomAD4 genome AF: 0.0394 AC: 6004 AN: 152214 Hom.: 291 Cov.: 33 AF XY: 0.0411 AC XY: 3056 AN XY: 74400

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.0191

Gnomad4 FIN AF: 0.00490

Gnomad4 NFE AF: 0.00713

Gnomad4 OTH AF: 0.0422

Alfa AF: 0.0149 Hom.: 45

Bravo AF: 0.0449

Asia WGS AF: 0.0880 AC: 306 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	1.1
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514490; hg19: chr16-80251265;