16-89977620-C-T

Variant names:

• chr16-89977620-C-T
• rs4408545
• ENST00000388970.8:n.170-19C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000437774.5(AFG3L1P):​n.165C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,330 control chromosomes in the GnomAD database, including 13,732 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 0.40 (13691 hom., cov: 32)
  • Exomes 𝑓: 0.48 (41 hom.)
• Consequence: AFG3L1P ENST00000437774.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 27 publications found

Genes affected

AFG3L1P (HGNC:):

AFG3L1P (HGNC:314): (AFG3 like matrix AAA peptidase subunit 1, pseudogene) Predicted to be involved in protein processing. Predicted to act upstream of or within cristae formation; mitochondrial fusion; and mitochondrial protein processing. Predicted to be located in mitochondrial inner membrane. Predicted to be part of m-AAA complex. [provided by Alliance of Genome Resources, Apr 2022]

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 (SAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000437774.5. 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
	AFG3L1P	NR_003226.1		n.202C>T		non_coding_transcript_exon	Exon 2 of 11
	AFG3L1P	NR_003227.1		n.187-58C>T		intron	N/A
	AFG3L1P	NR_003228.1		n.187-19C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFG3L1P	ENST00000388970.8	TSL:1	n.170-19C>T		intron	N/A
	AFG3L1P	ENST00000421164.5	TSL:1	n.119-19C>T		intron	N/A
	AFG3L1P	ENST00000421780.6	TSL:1	n.178-19C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60980 AN: 151832 Hom.: 13681 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.468

GnomAD4 exome AF: 0.481 AC: 182 AN: 378 Hom.: 41 Cov.: 0 AF XY: 0.496 AC XY: 111 AN XY: 224

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.476 AC: 177 AN: 372

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.401 AC: 61007 AN: 151952 Hom.: 13691 Cov.: 32 AF XY: 0.402 AC XY: 29812 AN XY: 74232

African (AFR) AF: 0.207 AC: 8563 AN: 41466

American (AMR) AF: 0.413 AC: 6310 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1970 AN: 3470

East Asian (EAS) AF: 0.189 AC: 975 AN: 5172

South Asian (SAS) AF: 0.577 AC: 2777 AN: 4814

European-Finnish (FIN) AF: 0.423 AC: 4446 AN: 10508

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34254 AN: 67948

Other (OTH) AF: 0.467 AC: 986 AN: 2112

Alfa AF: 0.463 Hom.: 15054

Bravo AF: 0.384

Asia WGS AF: 0.391 AC: 1358 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	0.95
DANN	Benign	0.31
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4408545; hg19: chr16-90044028;