1-66904609-C-T

Position:

• chr1-66904609-C-T

Variant summary

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

The NM_024763.5(DNAI4):​c.345+592G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,022 control chromosomes in the GnomAD database, including 47,738 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 0.79 (47738 hom., cov: 32)
• Consequence: DNAI4 NM_024763.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

Genes affected

DNAI4 (HGNC:26252): (dynein axonemal intermediate chain 4) Predicted to enable dynein heavy chain binding activity and dynein light chain binding activity. Predicted to be involved in axonemal dynein complex assembly and cilium movement. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be located in axoneme; dynein axonemal particle; and motile cilium. Predicted to be part of axonemal dynein complex. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAI4	NM_024763.5	c.345+592G>A		intron_variant		ENST00000371026.8	NP_079039.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAI4	ENST00000371026.8	c.345+592G>A		intron_variant		1	NM_024763.5	ENSP00000360065.3

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119799 AN: 151904 Hom.: 47676 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.789 AC: 119922 AN: 152022 Hom.: 47738 Cov.: 32 AF XY: 0.789 AC XY: 58590 AN XY: 74292

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.790

Alfa AF: 0.775 Hom.: 5714

Bravo AF: 0.805

Asia WGS AF: 0.872 AC: 3007 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.22

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: rs1925411; hg19: chr1-67370292;