dbSNP rs13475: SDHAF3:c.*202G>A (chr7-97181417-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145

Publications

7 publications found

Variant links:

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 links:

LOC124901704 (HGNC:):

LOC124901704 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDHAF3	NM_020186.3 link	c.*202G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000432641.3	NP_064571.1	Q9NRP4
LOC124901704	XR_007060445.1 link	n.132-1068C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SDHAF3	ENST00000432641.3 link	c.*202G>A	3_prime_UTR_variant	Exon 2 of 2	1	NM_020186.3	ENSP00000414066.2	Q9NRP4
SDHAF3	ENST00000479853.1 link	n.544G>A	non_coding_transcript_exon_variant	Exon 2 of 2	2
SDHAF3	ENST00000360382.4 link	c.*453G>A	3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000353548.4	F8W9V1

Frequencies

GnomAD3 genomes

AF:

0.589

AC:

89414

AN:

151846

Hom.:

26519

Cov.:

show subpopulations

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.:

AF XY:

0.606

AC XY:

86287

AN XY:

142312

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

3076

6153

9229

12306

15382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

650

1300

1950

2600

3250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.589

AC:

89471

AN:

151964

Hom.:

26533

Cov.:

AF XY:

0.587

AC XY:

43590

AN XY:

74268

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1868

3735

5603

7470

9338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.94

(source)

DANN

Benign

0.43

PhyloP100

-0.14

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over