7-97119700-T-C

Position:

• chr7-97119700-T-C

Variant summary

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

The NM_020186.3(SDHAF3):​c.174+1803T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,000 control chromosomes in the GnomAD database, including 12,513 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 0.40 (12513 hom., cov: 32)
• Consequence: SDHAF3 NM_020186.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

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]

SDHAF3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDHAF3	NM_020186.3	c.174+1803T>C		intron_variant		ENST00000432641.3	NP_064571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDHAF3	ENST00000432641.3	c.174+1803T>C		intron_variant		1	NM_020186.3	ENSP00000414066.2
SDHAF3	ENST00000360382.4	c.174+1803T>C		intron_variant		2		ENSP00000353548.4
SDHAF3	ENST00000489852.1	n.197+1803T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61148 AN: 151880 Hom.: 12495 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.403 AC: 61213 AN: 152000 Hom.: 12513 Cov.: 32 AF XY: 0.404 AC XY: 30052 AN XY: 74298

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.412

Alfa AF: 0.369 Hom.: 16508

Bravo AF: 0.410

Asia WGS AF: 0.467 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7794886; hg19: chr7-96749012;