rs7249111

Variant names:

• chr19-8313986-G-A
• rs7249111
• NM_005001.5:c.252-2391C>T

Variant summary

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

The NM_005001.5(NDUFA7):​c.252-2391C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,216 control chromosomes in the GnomAD database, including 3,893 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 0.15 (3893 hom., cov: 33)
• Consequence: NDUFA7 NM_005001.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 4 publications found

Genes affected

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]

ENSG00000167774 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFA7	NM_005001.5	c.252-2391C>T		intron_variant	Intron 3 of 3	ENST00000301457.3	NP_004992.2
NDUFA7	NR_135539.2	n.269-2391C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFA7	ENST00000301457.3	c.252-2391C>T		intron_variant	Intron 3 of 3	1	NM_005001.5	ENSP00000301457.1
ENSG00000167774	ENST00000598884.1	n.252-2391C>T		intron_variant	Intron 3 of 4	4		ENSP00000470609.1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23090 AN: 152098 Hom.: 3874 Cov.: 33

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.152 AC: 23152 AN: 152216 Hom.: 3893 Cov.: 33 AF XY: 0.153 AC XY: 11378 AN XY: 74438

African (AFR) AF: 0.417 AC: 17283 AN: 41478

American (AMR) AF: 0.0769 AC: 1176 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3472

East Asian (EAS) AF: 0.0898 AC: 466 AN: 5188

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4830

European-Finnish (FIN) AF: 0.0299 AC: 317 AN: 10616

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0352 AC: 2395 AN: 68020

Other (OTH) AF: 0.122 AC: 259 AN: 2116

Alfa AF: 0.0706 Hom.: 4467

Bravo AF: 0.164

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.33
PhyloP100		-0.95
Mutation Taster		=100/0	polymorphism (auto)

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: rs7249111; hg19: chr19-8378870;