7-97169870-A-T

Position:

• chr7-97169870-A-T

Variant summary

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

The ENST00000432641.3(SDHAF3):​c.175-11142A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 152,058 control chromosomes in the GnomAD database, including 42,104 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 0.74 (42104 hom., cov: 33)
• Consequence: SDHAF3 ENST00000432641.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDHAF3	NM_020186.3	c.175-11142A>T		intron_variant		ENST00000432641.3	NP_064571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDHAF3	ENST00000432641.3	c.175-11142A>T		intron_variant		1	NM_020186.3	ENSP00000414066	P1
SDHAF3	ENST00000360382.4	c.*48-11142A>T		intron_variant		2		ENSP00000353548
SDHAF3	ENST00000479853.1	n.139-11142A>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112942 AN: 151942 Hom.: 42072 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.743 AC: 113026 AN: 152058 Hom.: 42104 Cov.: 33 AF XY: 0.741 AC XY: 55068 AN XY: 74330

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.728

Alfa AF: 0.693 Hom.: 2325

Bravo AF: 0.741

Asia WGS AF: 0.643 AC: 2219 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.61

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: rs10256036; hg19: chr7-96799182;