rs6006473

chr22-43997195-C-T

Variant summary

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

The ENST00000465768.1(SAMM50):n.79+6789C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,054 control chromosomes in the GnomAD database, including 17,409 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 0.47 (17409 hom., cov: 33)
• Consequence: SAMM50 ENST00000465768.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMM50	ENST00000465768.1	n.79+6789C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71358 AN: 151936 Hom.: 17402 Cov.: 33

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.469 AC: 71388 AN: 152054 Hom.: 17409 Cov.: 33 AF XY: 0.473 AC XY: 35184 AN XY: 74330

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.450

Alfa AF: 0.414 Hom.: 6399

Bravo AF: 0.475

Asia WGS AF: 0.483 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.48
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6006473; hg19: chr22-44393075;