X-37841795-G-A

Variant names:

• chrX-37841795-G-A
• rs11771
• NM_006520.3:c.183C>T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_006520.3(DYNLT3):​c.183C>T​(p.Ala61Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,169,836 control chromosomes in the GnomAD database, including 19,938 homozygotes. There are 69,861 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.31 (5606 hom., 9496 hem., cov: 22)
  • Exomes 𝑓: 0.18 (14332 hom. 60365 hem.)
• Consequence: DYNLT3 NM_006520.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.608
• Publications: 12 publications found

Genes affected

DYNLT3 (HGNC:11694): (dynein light chain Tctex-type 3) This gene encodes a member of a subclass of dynein light chains. The encoded protein homodimerizes and forms the light chain component of the cytoplasmic dynein motor protein complex. This protein may be important for binding dynein to specific cargos including the spindle checkpoint protein BUB3. This protein may also function independently of dynein as a transcriptional modulator. Pseudogenes of this gene are found on chromosomes 2 and 20.[provided by RefSeq, Mar 2010]

ENSG00000250349 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BP6: Variant X-37841795-G-A is Benign according to our data. Variant chrX-37841795-G-A is described in ClinVar as Benign. ClinVar VariationId is 402816.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.608 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006520.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLT3	NM_006520.3	MANE Select	c.183C>T	p.Ala61Ala	synonymous	Exon 3 of 5	NP_006511.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLT3	ENST00000378578.9	TSL:1 MANE Select	c.183C>T	p.Ala61Ala	synonymous	Exon 3 of 5	ENSP00000367841.4
	ENSG00000250349	ENST00000465127.1	TSL:5	c.171+415795G>A		intron	N/A	ENSP00000417050.1
	DYNLT3	ENST00000378581.7	TSL:2	c.183C>T	p.Ala61Ala	synonymous	Exon 3 of 6	ENSP00000367844.3

Frequencies

GnomAD3 genomes AF: 0.308 AC: 33795 AN: 109893 Hom.: 5607 Cov.: 22

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.214

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.264

GnomAD2 exomes AF: 0.218 AC: 38439 AN: 176427 AF XY: 0.202

Gnomad AFR exome AF: 0.660

Gnomad AMR exome AF: 0.207

Gnomad ASJ exome AF: 0.139

Gnomad EAS exome AF: 0.229

Gnomad FIN exome AF: 0.193

Gnomad NFE exome AF: 0.156

Gnomad OTH exome AF: 0.197

GnomAD4 exome AF: 0.178 AC: 188160 AN: 1059891 Hom.: 14332 Cov.: 29 AF XY: 0.178 AC XY: 60365 AN XY: 338771

African (AFR) AF: 0.659 AC: 17084 AN: 25919

American (AMR) AF: 0.211 AC: 7284 AN: 34485

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 2689 AN: 18557

East Asian (EAS) AF: 0.269 AC: 7957 AN: 29549

South Asian (SAS) AF: 0.248 AC: 12098 AN: 48770

European-Finnish (FIN) AF: 0.192 AC: 7548 AN: 39275

Middle Eastern (MID) AF: 0.227 AC: 905 AN: 3989

European-Non Finnish (NFE) AF: 0.152 AC: 123975 AN: 815187

Other (OTH) AF: 0.195 AC: 8620 AN: 44160

GnomAD4 genome AF: 0.308 AC: 33827 AN: 109945 Hom.: 5606 Cov.: 22 AF XY: 0.294 AC XY: 9496 AN XY: 32259

African (AFR) AF: 0.646 AC: 19398 AN: 30043

American (AMR) AF: 0.225 AC: 2327 AN: 10359

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 363 AN: 2626

East Asian (EAS) AF: 0.227 AC: 792 AN: 3489

South Asian (SAS) AF: 0.257 AC: 666 AN: 2592

European-Finnish (FIN) AF: 0.188 AC: 1082 AN: 5765

Middle Eastern (MID) AF: 0.226 AC: 48 AN: 212

European-Non Finnish (NFE) AF: 0.164 AC: 8647 AN: 52673

Other (OTH) AF: 0.260 AC: 393 AN: 1509

Alfa AF: 0.231 Hom.: 2182

Bravo AF: 0.327

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

not provided Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	4.1
DANN	Benign	0.63
PhyloP100		-0.61
Mutation Taster		=99/1	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: rs11771; hg19: chrX-37701048; COSMIC: COSV66079168;