17-74309977-CCT-C

Position:

• chr17-74309977-CCT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000311014.11(DNAI2):​c.1348-34_1348-33del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 1,612,936 control chromosomes in the GnomAD database, including 661,008 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.78 (50201 hom., cov: 0)
  • Exomes 𝑓: 0.91 (610807 hom.)
• Consequence: DNAI2 ENST00000311014.11 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0410

Genes affected

DNAI2 (HGNC:18744): (dynein axonemal intermediate chain 2) The protein encoded by this gene belongs to the dynein intermediate chain family, and is part of the dynein complex of respiratory cilia and sperm flagella. Mutations in this gene are associated with primary ciliary dyskinesia type 9. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-74309977-CCT-C is Benign according to our data. Variant chr17-74309977-CCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 261640.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAI2	NM_023036.6	c.1348-34_1348-33del		intron_variant		ENST00000311014.11	NP_075462.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAI2	ENST00000311014.11	c.1348-34_1348-33del		intron_variant		1	NM_023036.6	ENSP00000308312	P2

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119062 AN: 151746 Hom.: 50197 Cov.: 0

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.803

GnomAD3 exomes AF: 0.885 AC: 221102 AN: 249966 Hom.: 99781 AF XY: 0.890 AC XY: 120639 AN XY: 135482

Gnomad AFR exome AF: 0.420

Gnomad AMR exome AF: 0.940

Gnomad ASJ exome AF: 0.897

Gnomad EAS exome AF: 0.933

Gnomad SAS exome AF: 0.865

Gnomad FIN exome AF: 0.903

Gnomad NFE exome AF: 0.925

Gnomad OTH exome AF: 0.898

GnomAD4 exome AF: 0.911 AC: 1330783 AN: 1461072 Hom.: 610807 AF XY: 0.911 AC XY: 662209 AN XY: 726838

Gnomad4 AFR exome AF: 0.423

Gnomad4 AMR exome AF: 0.933

Gnomad4 ASJ exome AF: 0.900

Gnomad4 EAS exome AF: 0.925

Gnomad4 SAS exome AF: 0.867

Gnomad4 FIN exome AF: 0.908

Gnomad4 NFE exome AF: 0.930

Gnomad4 OTH exome AF: 0.883

GnomAD4 genome AF: 0.784 AC: 119082 AN: 151864 Hom.: 50201 Cov.: 0 AF XY: 0.787 AC XY: 58450 AN XY: 74234

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.801

Alfa AF: 0.866 Hom.: 10674

Bravo AF: 0.769

Asia WGS AF: 0.860 AC: 2990 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		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: rs35732837; hg19: chr17-72306116;