16-80549602-G-T

Variant names:

• chr16-80549602-G-T
• NM_130897.3:c.198G>T
• DYNLRB2 p.Leu66Leu

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_130897.3(DYNLRB2):​c.198G>T​(p.Leu66Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L66L) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DYNLRB2 NM_130897.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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.198G>T	p.Leu66Leu	synonymous	Exon 3 of 4	NP_570967.1	A0A140VJH9
	DYNLRB2	NM_001305017.2		c.285G>T	p.Leu95Leu	synonymous	Exon 3 of 4	NP_001291946.1	H3BQI1
	DYNLRB2	NR_130942.2		n.823G>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.198G>T	p.Leu66Leu	synonymous	Exon 3 of 4	ENSP00000302936.6	Q8TF09
	DYNLRB2	ENST00000338542.9	TSL:1	n.*123G>T		non_coding_transcript_exon	Exon 4 of 5	ENSP00000342009.5	Q7Z4M1
	DYNLRB2	ENST00000338542.9	TSL:1	n.*123G>T		3_prime_UTR	Exon 4 of 5	ENSP00000342009.5	Q7Z4M1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.12
DANN	Benign	0.74
PhyloP100		-1.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-80583499;