rs13475

Positions:

• chr7-97181417-G-A
• chr7-97181417-G-T

Variant summary

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

The NM_020186.3(SDHAF3):​c.*202G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 426,262 control chromosomes in the GnomAD database, including 77,639 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 0.59 (26533 hom., cov: 32)
  • Exomes 𝑓: 0.61 (51106 hom.)
• Consequence: SDHAF3 NM_020186.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

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]

LOC124901704 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDHAF3	NM_020186.3	c.*202G>A		3_prime_UTR_variant	2/2	ENST00000432641.3	NP_064571.1
LOC124901704	XR_007060445.1	n.132-1068C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDHAF3	ENST00000432641.3	c.*202G>A		3_prime_UTR_variant	2/2	1	NM_020186.3	ENSP00000414066	P1
SDHAF3	ENST00000360382.4	c.*453G>A		3_prime_UTR_variant	3/3	2		ENSP00000353548
SDHAF3	ENST00000479853.1	n.544G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89414 AN: 151846 Hom.: 26519 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.584

GnomAD4 exome AF: 0.608 AC: 166708 AN: 274298 Hom.: 51106 Cov.: 4 AF XY: 0.606 AC XY: 86287 AN XY: 142312

Gnomad4 AFR exome AF: 0.524

Gnomad4 AMR exome AF: 0.584

Gnomad4 ASJ exome AF: 0.560

Gnomad4 EAS exome AF: 0.477

Gnomad4 SAS exome AF: 0.575

Gnomad4 FIN exome AF: 0.622

Gnomad4 NFE exome AF: 0.633

Gnomad4 OTH exome AF: 0.602

GnomAD4 genome AF: 0.589 AC: 89471 AN: 151964 Hom.: 26533 Cov.: 32 AF XY: 0.587 AC XY: 43590 AN XY: 74268

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.581

Alfa AF: 0.610 Hom.: 8905

Bravo AF: 0.581

Asia WGS AF: 0.522 AC: 1814 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.94
DANN	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs13475; hg19: chr7-96810729;