Variant 16-80549600-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_130897.3(DYNLRB2):c.196C>T(p.Leu66=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,611,236 control chromosomes in the GnomAD database, including 40,983 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4040 hom., cov: 33)

Exomes 𝑓: 0.22 ( 36943 hom. )

Consequence

DYNLRB2
NM_130897.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.73

Variant links:

Genes affected

DYNLRB2 (HGNC:15467): (dynein light chain roadblock-type 2) Predicted to enable dynein intermediate chain binding activity. Predicted to be involved in microtubule-based movement. Predicted to be located in ciliary tip. Predicted to be part of cytoplasmic dynein complex. Predicted to be active in centrosome and cytoplasm. Biomarker of hepatocellular carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

DYNLRB2 links:

(HGNC:):

links:

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

DYNLRB2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 16-80549600-C-T is Benign according to our data. Variant chr16-80549600-C-T is described in ClinVar as [Benign]. Clinvar id is 402815.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.73 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DYNLRB2	NM_130897.3 linkuse as main transcript	c.196C>T	p.Leu66=	synonymous_variant	3/4	ENST00000305904.11
DYNLRB2-AS1	NR_120307.1 linkuse as main transcript	n.107+13429G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
DYNLRB2	ENST00000305904.11 linkuse as main transcript	c.196C>T	p.Leu66=	synonymous_variant	3/4	1	NM_130897.3	P1
	ENST00000568275.1 linkuse as main transcript	n.192-1416G>A		intron_variant, non_coding_transcript_variant		4
DYNLRB2-AS1	ENST00000668341.1 linkuse as main transcript	n.272+13429G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34256

AN:

152006

Hom.:

4037

Cov.:

show subpopulations

Gnomad AFR

AF:

0.254

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.0102

Gnomad SAS

AF:

0.0621

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.258

GnomAD3 exomes

AF:

0.184

AC:

46184

AN:

250944

Hom.:

5248

AF XY:

0.183

AC XY:

24803

AN XY:

135644

show subpopulations

Gnomad AFR exome

AF:

0.255

Gnomad AMR exome

AF:

0.127

Gnomad ASJ exome

AF:

0.262

Gnomad EAS exome

AF:

0.00913

Gnomad SAS exome

AF:

0.0636

Gnomad FIN exome

AF:

0.218

Gnomad NFE exome

AF:

0.236

Gnomad OTH exome

AF:

0.229

GnomAD4 exome

AF:

0.216

AC:

314861

AN:

1459112

Hom.:

36943

Cov.:

AF XY:

0.212

AC XY:

153966

AN XY:

725820

show subpopulations

Gnomad4 AFR exome

AF:

0.260

Gnomad4 AMR exome

AF:

0.137

Gnomad4 ASJ exome

AF:

0.261

Gnomad4 EAS exome

AF:

0.00683

Gnomad4 SAS exome

AF:

0.0643

Gnomad4 FIN exome

AF:

0.221

Gnomad4 NFE exome

AF:

0.235

Gnomad4 OTH exome

AF:

0.216

GnomAD4 genome

AF:

0.225

AC:

34279

AN:

152124

Hom.:

4040

Cov.:

AF XY:

0.220

AC XY:

16391

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.255

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.263

Gnomad4 EAS

AF:

0.00985

Gnomad4 SAS

AF:

0.0618

Gnomad4 FIN

AF:

0.222

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.241

Hom.:

2526

Bravo

AF:

0.227

Asia WGS

AF:

0.0560

AC:

197

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

7.5

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over