9-7822519-T-C

Variant names:

• chr9-7822519-T-C
• rs1029089
• ENST00000469050.1:n.164+11406A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000469050.1(DMAC1):​n.164+11406A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,004 control chromosomes in the GnomAD database, including 29,252 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 0.61 (29252 hom., cov: 33)
• Consequence: DMAC1 ENST00000469050.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530
• Publications: 4 publications found

Genes affected

DMAC1 (HGNC:30536): (distal membrane arm assembly component 1) Involved in mitochondrial respiratory chain complex I assembly. Located in mitochondrial inner membrane. Colocalizes with mitochondrial respiratory chain complex I. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000469050.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMAC1	ENST00000469050.1	TSL:3	n.164+11406A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92149 AN: 151886 Hom.: 29185 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.607 AC: 92278 AN: 152004 Hom.: 29252 Cov.: 33 AF XY: 0.609 AC XY: 45248 AN XY: 74296

African (AFR) AF: 0.781 AC: 32394 AN: 41482

American (AMR) AF: 0.599 AC: 9137 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1827 AN: 3472

East Asian (EAS) AF: 0.751 AC: 3877 AN: 5164

South Asian (SAS) AF: 0.626 AC: 3017 AN: 4822

European-Finnish (FIN) AF: 0.562 AC: 5936 AN: 10558

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34437 AN: 67952

Other (OTH) AF: 0.573 AC: 1204 AN: 2102

Alfa AF: 0.526 Hom.: 7687

Bravo AF: 0.615

Asia WGS AF: 0.709 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	16
DANN	Benign	0.82
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs1029089; hg19: chr9-7822519;