7-97152992-A-T

Variant names:

• chr7-97152992-A-T
• rs2103212
• NM_020186.3:c.175-28020A>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.175-28020A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,288 control chromosomes in the GnomAD database, including 372 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 0.067 (372 hom., cov: 33)
• Consequence: SDHAF3 NM_020186.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 3 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]

LOC107984034 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDHAF3	NM_020186.3	c.175-28020A>T		intron_variant	Intron 1 of 1	ENST00000432641.3	NP_064571.1
LOC107984034	XR_001745291.1	n.227-4268A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDHAF3	ENST00000432641.3	c.175-28020A>T		intron_variant	Intron 1 of 1	1	NM_020186.3	ENSP00000414066.2
SDHAF3	ENST00000360382.4	c.*47+16525A>T		intron_variant	Intron 2 of 2	2		ENSP00000353548.4
SDHAF3	ENST00000479853.1	n.138+10174A>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0666 AC: 10141 AN: 152170 Hom.: 372 Cov.: 33

Gnomad AFR AF: 0.0266

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.0662

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0797

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0666 AC: 10146 AN: 152288 Hom.: 372 Cov.: 33 AF XY: 0.0695 AC XY: 5176 AN XY: 74464

African (AFR) AF: 0.0266 AC: 1105 AN: 41566

American (AMR) AF: 0.0661 AC: 1010 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3470

East Asian (EAS) AF: 0.0663 AC: 344 AN: 5188

South Asian (SAS) AF: 0.113 AC: 546 AN: 4820

European-Finnish (FIN) AF: 0.110 AC: 1165 AN: 10612

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0797 AC: 5419 AN: 68022

Other (OTH) AF: 0.0738 AC: 156 AN: 2114

Alfa AF: 0.0335 Hom.: 16

Bravo AF: 0.0625

Asia WGS AF: 0.0930 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.41
PhyloP100		0.22
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: rs2103212; hg19: chr7-96782304;