11-73958000-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_153614.4(DNAJB13):c.69-317G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,036 control chromosomes in the GnomAD database, including 21,834 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.53 (21834 hom., cov: 32)
• Consequence: DNAJB13 NM_153614.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.19

Genes affected

DNAJB13 (HGNC:30718): (DnaJ heat shock protein family (Hsp40) member B13) This gene encodes a member of the heat shock protein 40 co-chaperone family which is produced in large amounts in the testis and is located on the radial spokes of the axoneme in human sperm flagella and other flagellar structures. The encoded protein associates with the sperm annulus, as part of the septin complex, through direct interaction with septin 4, during sperm terminal differentiation. Naturally occurring mutations in this gene are associated with primary ciliary dyskinesia and male infertility. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 11-73958000-G-C is Benign according to our data. Variant chr11-73958000-G-C is described in ClinVar as [Benign]. Clinvar id is 1235737.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAJB13	NM_153614.4	c.69-317G>C		intron_variant		ENST00000339764.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAJB13	ENST00000339764.6	c.69-317G>C		intron_variant		1	NM_153614.4	P1
DNAJB13	ENST00000535730.1	n.113-317G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79779 AN: 151918 Hom.: 21815 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.525 AC: 79841 AN: 152036 Hom.: 21834 Cov.: 32 AF XY: 0.524 AC XY: 38918 AN XY: 74308

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.511

Alfa AF: 0.337 Hom.: 816

Bravo AF: 0.528

Asia WGS AF: 0.526 AC: 1829 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 20, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.12
Dann	Benign	0.43

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

Other links and lift over

dbSNP: rs612914; hg19: chr11-73669045; COSMIC: COSV60268925;