22-43998522-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465768.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMM50	ENST00000465768.1	TSL:3	n.79+8116C>T		intron	N/A

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

African (AFR) AF: 0.180 AC: 7460 AN: 41492

American (AMR) AF: 0.301 AC: 4594 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2004 AN: 5160

South Asian (SAS) AF: 0.201 AC: 969 AN: 4822

European-Finnish (FIN) AF: 0.230 AC: 2434 AN: 10570

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12245 AN: 68002

Other (OTH) AF: 0.221 AC: 467 AN: 2112

Alfa AF: 0.186 Hom.: 7462

Bravo AF: 0.210

Asia WGS AF: 0.272 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2073080; hg19: chr22-44394402;