rs13475

Variant names:

• chr7-97181417-G-A
• rs13475
• NM_020186.3:c.*202G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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]

LOC124901704 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020186.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDHAF3	NM_020186.3	MANE Select	c.*202G>A		3_prime_UTR	Exon 2 of 2	NP_064571.1	Q9NRP4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDHAF3	ENST00000432641.3	TSL:1 MANE Select	c.*202G>A		3_prime_UTR	Exon 2 of 2	ENSP00000414066.2	Q9NRP4
	SDHAF3	ENST00000360382.4	TSL:2	c.*453G>A		3_prime_UTR	Exon 3 of 3	ENSP00000353548.4	F8W9V1
	SDHAF3	ENST00000479853.1	TSL:2	n.544G>A		non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.524 AC: 3921 AN: 7486

American (AMR) AF: 0.584 AC: 5462 AN: 9350

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 5084 AN: 9082

East Asian (EAS) AF: 0.477 AC: 9835 AN: 20602

South Asian (SAS) AF: 0.575 AC: 9853 AN: 17136

European-Finnish (FIN) AF: 0.622 AC: 11446 AN: 18414

Middle Eastern (MID) AF: 0.616 AC: 781 AN: 1268

European-Non Finnish (NFE) AF: 0.633 AC: 110263 AN: 174254

Other (OTH) AF: 0.602 AC: 10063 AN: 16706

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

African (AFR) AF: 0.516 AC: 21374 AN: 41414

American (AMR) AF: 0.603 AC: 9219 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3470

East Asian (EAS) AF: 0.508 AC: 2620 AN: 5160

South Asian (SAS) AF: 0.576 AC: 2775 AN: 4818

European-Finnish (FIN) AF: 0.636 AC: 6724 AN: 10566

Middle Eastern (MID) AF: 0.617 AC: 179 AN: 290

European-Non Finnish (NFE) AF: 0.630 AC: 42781 AN: 67948

Other (OTH) AF: 0.581 AC: 1227 AN: 2112

Alfa AF: 0.611 Hom.: 13683

Bravo AF: 0.581

Asia WGS AF: 0.522 AC: 1814 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.94
DANN	Benign	0.43
PhyloP100		-0.14
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: rs13475; hg19: chr7-96810729;