rs4408545

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-89977620-C-G
• chr16-89977620-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000388970.8(AFG3L1P):​n.170-19C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: AFG3L1P ENST00000388970.8 intron
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AFG3L1P	NR_003226.1	n.202C>G		non_coding_transcript_exon_variant	Exon 2 of 11
AFG3L1P	NR_003227.1	n.187-58C>G		intron_variant	Intron 1 of 9
AFG3L1P	NR_003228.1	n.187-19C>G		intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AFG3L1P	ENST00000388970.8	n.170-19C>G		intron_variant	Intron 1 of 12	1
AFG3L1P	ENST00000421164.5	n.119-19C>G		intron_variant	Intron 1 of 5	1
AFG3L1P	ENST00000421780.6	n.178-19C>G		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 15054

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.98
DANN	Benign	0.33
PhyloP100		-0.48
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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;