chr1-85003931-G-A

Variant names:

• chr1-85003931-G-A
• rs1837329
• ENST00000370596.5:c.-15+4593G>A

Variant summary

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

The ENST00000370596.5(DNAI3):​c.-15+4593G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,112 control chromosomes in the GnomAD database, including 43,758 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 (43758 hom., cov: 32)
• Consequence: DNAI3 ENST00000370596.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 1 publications found

Genes affected

DNAI3 (HGNC:30711): (dynein axonemal intermediate chain 3) Enables Arp2/3 complex binding activity. Involved in negative regulation of Arp2/3 complex-mediated actin nucleation and negative regulation of cell migration. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000295769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAI3	ENST00000370596.5	c.-15+4593G>A		intron_variant	Intron 1 of 21	5		ENSP00000359628.1
ENSG00000295769	ENST00000732651.1	n.139+6572G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114958 AN: 151994 Hom.: 43741 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.756 AC: 115021 AN: 152112 Hom.: 43758 Cov.: 32 AF XY: 0.756 AC XY: 56220 AN XY: 74372

African (AFR) AF: 0.667 AC: 27647 AN: 41432

American (AMR) AF: 0.727 AC: 11106 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2787 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3786 AN: 5174

South Asian (SAS) AF: 0.807 AC: 3893 AN: 4824

European-Finnish (FIN) AF: 0.800 AC: 8472 AN: 10590

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.805 AC: 54734 AN: 68022

Other (OTH) AF: 0.754 AC: 1595 AN: 2114

Alfa AF: 0.780 Hom.: 5447

Bravo AF: 0.747

Asia WGS AF: 0.729 AC: 2535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.9
DANN	Benign	0.28
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1837329; hg19: chr1-85469614;