rs4785763

Variant names:

• chr16-90000528-A-C
• rs4785763
• ENST00000355531.7:n.1304A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-90000528-A-C
• chr16-90000528-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000355531.7(AFG3L1P):​n.1304A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.692 in 157,502 control chromosomes in the GnomAD database, including 37,786 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 0.69 (36454 hom., cov: 32)
  • Exomes 𝑓: 0.70 (1332 hom.)
• Consequence: AFG3L1P ENST00000355531.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.88
• Publications: 80 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AFG3L1P	NR_003228.1	n.1682A>C		non_coding_transcript_exon_variant	Exon 13 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AFG3L1P	ENST00000355531.7	n.1304A>C		non_coding_transcript_exon_variant	Exon 7 of 7	1
AFG3L1P	ENST00000388970.8	n.1665A>C		non_coding_transcript_exon_variant	Exon 13 of 13	1
AFG3L1P	ENST00000454997.1	n.1694A>C		non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105151 AN: 151914 Hom.: 36429 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.714

GnomAD4 exome AF: 0.696 AC: 3807 AN: 5470 Hom.: 1332 Cov.: 0 AF XY: 0.691 AC XY: 2028 AN XY: 2934

African (AFR) AF: 0.734 AC: 69 AN: 94

American (AMR) AF: 0.700 AC: 42 AN: 60

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 68 AN: 110

East Asian (EAS) AF: 0.872 AC: 546 AN: 626

South Asian (SAS) AF: 0.842 AC: 32 AN: 38

European-Finnish (FIN) AF: 0.742 AC: 787 AN: 1060

Middle Eastern (MID) AF: 0.667 AC: 16 AN: 24

European-Non Finnish (NFE) AF: 0.648 AC: 2045 AN: 3156

Other (OTH) AF: 0.669 AC: 202 AN: 302

GnomAD4 genome AF: 0.692 AC: 105220 AN: 152032 Hom.: 36454 Cov.: 32 AF XY: 0.699 AC XY: 51931 AN XY: 74302

African (AFR) AF: 0.682 AC: 28258 AN: 41460

American (AMR) AF: 0.753 AC: 11508 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2340 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3787 AN: 5140

South Asian (SAS) AF: 0.753 AC: 3627 AN: 4818

European-Finnish (FIN) AF: 0.738 AC: 7806 AN: 10574

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45583 AN: 67966

Other (OTH) AF: 0.714 AC: 1507 AN: 2110

Alfa AF: 0.677 Hom.: 166854

Bravo AF: 0.687

Asia WGS AF: 0.740 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	8.1
DANN	Benign	0.62
PhyloP100		6.9

Splicing

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

Other links and lift over

dbSNP: rs4785763; hg19: chr16-90066936;