rs3793472

Variant names:

• chr9-34492215-G-A
• rs3793472
• NM_012144.4:c.681+661G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-34492215-G-A
• chr9-34492215-G-C
• chr9-34492215-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012144.4(DNAI1):​c.681+661G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 151,534 control chromosomes in the GnomAD database, including 44,079 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (44079 hom., cov: 27)
• Consequence: DNAI1 NM_012144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584
• Publications: 5 publications found

Genes affected

DNAI1 (HGNC:2954): (dynein axonemal intermediate chain 1) This gene encodes a member of the dynein intermediate chain family. The encoded protein is part of the dynein complex in respiratory cilia. The inner- and outer-arm dyneins, which bridge between the doublet microtubules in axonemes, are the force-generating proteins responsible for the sliding movement in axonemes. The intermediate and light chains, thought to form the base of the dynein arm, help mediate attachment and may also participate in regulating dynein activity. Mutations in this gene result in abnormal ciliary ultrastructure and function associated with primary ciliary dyskinesia and Kartagener syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

DNAI1 Gene-Disease associations (from GenCC):

• primary ciliary dyskinesia 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, PanelApp Australia
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAI1	NM_012144.4	c.681+661G>A		intron_variant	Intron 8 of 19	ENST00000242317.9	NP_036276.1
DNAI1	NM_001281428.2	c.693+661G>A		intron_variant	Intron 8 of 19		NP_001268357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAI1	ENST00000242317.9	c.681+661G>A		intron_variant	Intron 8 of 19	1	NM_012144.4	ENSP00000242317.4

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115304 AN: 151414 Hom.: 44020 Cov.: 27

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.762 AC: 115419 AN: 151534 Hom.: 44079 Cov.: 27 AF XY: 0.765 AC XY: 56618 AN XY: 74040

African (AFR) AF: 0.787 AC: 32482 AN: 41288

American (AMR) AF: 0.733 AC: 11170 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2419 AN: 3466

East Asian (EAS) AF: 0.845 AC: 4327 AN: 5118

South Asian (SAS) AF: 0.873 AC: 4190 AN: 4800

European-Finnish (FIN) AF: 0.770 AC: 8092 AN: 10510

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50188 AN: 67826

Other (OTH) AF: 0.744 AC: 1553 AN: 2086

Alfa AF: 0.740 Hom.: 151743

Bravo AF: 0.755

Asia WGS AF: 0.847 AC: 2943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.53
PhyloP100		0.58
Mutation Taster		=100/0	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: rs3793472; hg19: chr9-34492213;