rs10815701

Variant names:

• chr9-7871163-A-G
• rs10815701
• ENST00000469050.1:n.82+17136T>C

Variant summary

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

The ENST00000469050.1(DMAC1):​n.82+17136T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,096 control chromosomes in the GnomAD database, including 4,224 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 0.23 (4224 hom., cov: 31)
• Consequence: DMAC1 ENST00000469050.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 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
DMAC1	ENST00000469050.1	n.82+17136T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34826 AN: 151978 Hom.: 4213 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.229 AC: 34863 AN: 152096 Hom.: 4224 Cov.: 31 AF XY: 0.233 AC XY: 17293 AN XY: 74346

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.220

Alfa AF: 0.235 Hom.: 9311

Bravo AF: 0.226

Asia WGS AF: 0.296 AC: 1029 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	0.25
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10815701; hg19: chr9-7871163;