rs11866734

Variant names:

• chr16-80549600-C-T
• rs11866734
• NM_130897.3:c.196C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-80549600-C-T
• chr16-80549600-C-A
• chr16-80549600-C-G

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_130897.3(DYNLRB2):​c.196C>T​(p.Leu66Leu) 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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 2.73
• Publications: 10 publications found

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

ACMG classification

Our verdict: Benign. The variant received -19 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 VariationId is 402815.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_130897.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2	NM_130897.3	MANE Select	c.196C>T	p.Leu66Leu	synonymous	Exon 3 of 4	NP_570967.1	A0A140VJH9
	DYNLRB2	NM_001305017.2		c.283C>T	p.Leu95Leu	synonymous	Exon 3 of 4	NP_001291946.1	H3BQI1
	DYNLRB2	NR_130942.2		n.821C>T		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2	ENST00000305904.11	TSL:1 MANE Select	c.196C>T	p.Leu66Leu	synonymous	Exon 3 of 4	ENSP00000302936.6	Q8TF09
	DYNLRB2	ENST00000338542.9	TSL:1	n.*121C>T		non_coding_transcript_exon	Exon 4 of 5	ENSP00000342009.5	Q7Z4M1
	DYNLRB2	ENST00000338542.9	TSL:1	n.*121C>T		3_prime_UTR	Exon 4 of 5	ENSP00000342009.5	Q7Z4M1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34256 AN: 152006 Hom.: 4037 Cov.: 33

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

GnomAD2 exomes AF: 0.184 AC: 46184 AN: 250944 AF XY: 0.183

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 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.: 32 AF XY: 0.212 AC XY: 153966 AN XY: 725820

African (AFR) AF: 0.260 AC: 8709 AN: 33446

American (AMR) AF: 0.137 AC: 6099 AN: 44624

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 6801 AN: 26046

East Asian (EAS) AF: 0.00683 AC: 271 AN: 39650

South Asian (SAS) AF: 0.0643 AC: 5526 AN: 85988

European-Finnish (FIN) AF: 0.221 AC: 11746 AN: 53268

Middle Eastern (MID) AF: 0.334 AC: 1920 AN: 5756

European-Non Finnish (NFE) AF: 0.235 AC: 260797 AN: 1110104

Other (OTH) AF: 0.216 AC: 12992 AN: 60230

GnomAD4 genome AF: 0.225 AC: 34279 AN: 152124 Hom.: 4040 Cov.: 33 AF XY: 0.220 AC XY: 16391 AN XY: 74372

African (AFR) AF: 0.255 AC: 10554 AN: 41468

American (AMR) AF: 0.197 AC: 3018 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.00985 AC: 51 AN: 5180

South Asian (SAS) AF: 0.0618 AC: 298 AN: 4824

European-Finnish (FIN) AF: 0.222 AC: 2355 AN: 10592

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16263 AN: 67984

Other (OTH) AF: 0.255 AC: 539 AN: 2114

Alfa AF: 0.243 Hom.: 2758

Bravo AF: 0.227

Asia WGS AF: 0.0560 AC: 197 AN: 3476

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	7.5
DANN	Benign	0.79
PhyloP100		2.7
Mutation Taster		=59/41	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11866734; hg19: chr16-80583497;