rs17387019

chr12-25111325-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018272.5(DNAI7):c.1779+447C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0566 in 152,212 control chromosomes in the GnomAD database, including 334 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 0.057 (334 hom., cov: 32)
• Consequence: DNAI7 NM_018272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

DNAI7 (HGNC:29599): (dynein axonemal intermediate chain 7) Predicted to enable beta-tubulin binding activity and microtubule binding activity. Predicted to be located in cilium; cytoplasm; and microtubule cytoskeleton. Predicted to be part of axonemal dynein complex. Predicted to be active in axoneme. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAI7	NM_018272.5	c.1779+447C>T		intron_variant		ENST00000395987.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAI7	ENST00000395987.8	c.1779+447C>T		intron_variant		1	NM_018272.5	A1

Frequencies

GnomAD3 genomes AF: 0.0567 AC: 8617 AN: 152094 Hom.: 333 Cov.: 32

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0566 AC: 8622 AN: 152212 Hom.: 334 Cov.: 32 AF XY: 0.0541 AC XY: 4024 AN XY: 74430

Gnomad4 AFR AF: 0.0172

Gnomad4 AMR AF: 0.0738

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0209

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0850

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0740 Hom.: 224

Bravo AF: 0.0585

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.042
Dann	Benign	0.42

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: rs17387019; hg19: chr12-25264259;