rs4740919

Variant names:

• chr9-7854892-G-A
• rs4740919
• ENST00000469050.1:n.83-20886C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-7854892-G-A
• chr9-7854892-G-C
• chr9-7854892-G-T

Variant summary

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

The ENST00000469050.1(DMAC1):​n.83-20886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,904 control chromosomes in the GnomAD database, including 5,134 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 0.25 (5134 hom., cov: 32)
• Consequence: DMAC1 ENST00000469050.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 0 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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.83-20886C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38449 AN: 151788 Hom.: 5123 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.253 AC: 38483 AN: 151904 Hom.: 5134 Cov.: 32 AF XY: 0.255 AC XY: 18956 AN XY: 74258

African (AFR) AF: 0.169 AC: 6991 AN: 41388

American (AMR) AF: 0.306 AC: 4677 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1810 AN: 5140

South Asian (SAS) AF: 0.334 AC: 1609 AN: 4814

European-Finnish (FIN) AF: 0.308 AC: 3251 AN: 10548

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18782 AN: 67966

Other (OTH) AF: 0.237 AC: 500 AN: 2106

Alfa AF: 0.223 Hom.: 1077

Bravo AF: 0.249

Asia WGS AF: 0.293 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs4740919; hg19: chr9-7854892;