22-43998522-C-T

Variant names:

• chr22-43998522-C-T
• rs2073080
• ENST00000465768.1:n.79+8116C>T

Variant summary

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

The ENST00000465768.1(SAMM50):​n.79+8116C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,104 control chromosomes in the GnomAD database, including 3,328 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 0.20 (3328 hom., cov: 32)
• Consequence: SAMM50 ENST00000465768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

Genes affected

SAMM50 (HGNC:24276): (SAMM50 sorting and assembly machinery component) This gene encodes a component of the Sorting and Assembly Machinery (SAM) of the mitochondrial outer membrane. The Sam complex functions in the assembly of beta-barrel proteins into the outer mitochondrial membrane.[provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMM50	ENST00000465768.1	n.79+8116C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30898 AN: 151986 Hom.: 3326 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.203 AC: 30902 AN: 152104 Hom.: 3328 Cov.: 32 AF XY: 0.209 AC XY: 15535 AN XY: 74336

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.221

Alfa AF: 0.180 Hom.: 3202

Bravo AF: 0.210

Asia WGS AF: 0.272 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2073080; hg19: chr22-44394402;