chr19-8309181-G-C

Variant names:

• chr19-8309181-G-C
• rs2232765
• ENST00000598884.1:n.*94-775C>G

Variant summary

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

The ENST00000598884.1(ENSG00000167774):​n.*94-775C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,574 control chromosomes in the GnomAD database, including 13,133 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 0.41 (13133 hom., cov: 31)
• Consequence: ENSG00000167774 ENST00000598884.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767
• Publications: 3 publications found

Genes affected

ENSG00000167774 (HGNC:):

NDUFA7 (HGNC:7691): (NADH:ubiquinone oxidoreductase subunit A7) This gene encodes a subunit of NADH:ubiquinone oxidoreductase (complex I), which is a multiprotein complex located in the inner mitochondrial membrane. Complex I functions in the transfer of electrons from NADH to the respiratory chain. [provided by RefSeq, Mar 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFA7	NR_135539.2	n.453-297C>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000167774	ENST00000598884.1	n.*94-775C>G		intron_variant	Intron 4 of 4	4		ENSP00000470609.1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62435 AN: 151456 Hom.: 13107 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.412 AC: 62509 AN: 151574 Hom.: 13133 Cov.: 31 AF XY: 0.418 AC XY: 30937 AN XY: 74024

African (AFR) AF: 0.476 AC: 19674 AN: 41330

American (AMR) AF: 0.350 AC: 5331 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.388 AC: 1990 AN: 5132

South Asian (SAS) AF: 0.540 AC: 2586 AN: 4790

European-Finnish (FIN) AF: 0.469 AC: 4916 AN: 10490

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25472 AN: 67846

Other (OTH) AF: 0.375 AC: 787 AN: 2096

Alfa AF: 0.396 Hom.: 1448

Bravo AF: 0.405

Asia WGS AF: 0.434 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		-0.77

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

Other links and lift over

dbSNP: rs2232765; hg19: chr19-8374065;