rs4398831

Variant names:

• chr7-97127745-T-C
• rs4398831
• NM_020186.3:c.174+9848T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-97127745-T-C
• chr7-97127745-T-G

Variant summary

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

The NM_020186.3(SDHAF3):​c.174+9848T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,062 control chromosomes in the GnomAD database, including 5,383 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 (5383 hom., cov: 31)
• Consequence: SDHAF3 NM_020186.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 2 publications found

Genes affected

SDHAF3 (HGNC:21752): (succinate dehydrogenase complex assembly factor 3) Predicted to be involved in mitochondrial respiratory chain complex II assembly; regulation of gluconeogenesis; and succinate metabolic process. Predicted to be located in mitochondrial matrix. Predicted to be active in mitochondrial intermembrane space. [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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDHAF3	NM_020186.3	c.174+9848T>C		intron_variant	Intron 1 of 1	ENST00000432641.3	NP_064571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDHAF3	ENST00000432641.3	c.174+9848T>C		intron_variant	Intron 1 of 1	1	NM_020186.3	ENSP00000414066.2
SDHAF3	ENST00000360382.4	c.175-8643T>C		intron_variant	Intron 1 of 2	2		ENSP00000353548.4
SDHAF3	ENST00000489852.1	n.197+9848T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38588 AN: 151944 Hom.: 5381 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.254 AC: 38594 AN: 152062 Hom.: 5383 Cov.: 31 AF XY: 0.254 AC XY: 18846 AN XY: 74322

African (AFR) AF: 0.149 AC: 6191 AN: 41510

American (AMR) AF: 0.243 AC: 3715 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3470

East Asian (EAS) AF: 0.125 AC: 644 AN: 5162

South Asian (SAS) AF: 0.271 AC: 1307 AN: 4826

European-Finnish (FIN) AF: 0.333 AC: 3514 AN: 10554

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21291 AN: 67962

Other (OTH) AF: 0.261 AC: 552 AN: 2114

Alfa AF: 0.288 Hom.: 12434

Bravo AF: 0.241

Asia WGS AF: 0.194 AC: 677 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	5.5
DANN	Benign	0.80
PhyloP100		0.094
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: rs4398831; hg19: chr7-96757057;