rs4785763

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

AFG3L1P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
AFG3L1P	NR_003228.1	n.1682A>C		non_coding_transcript_exon_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AFG3L1P	ENST00000355531.7	n.1304A>C		non_coding_transcript_exon_variant	7/7	1
AFG3L1P	ENST00000388970.7	n.1441A>C		non_coding_transcript_exon_variant	12/12	1
AFG3L1P	ENST00000454997.1	n.1694A>C		non_coding_transcript_exon_variant	3/3	2
AFG3L1P	ENST00000557444.5	n.2307A>C		non_coding_transcript_exon_variant	17/17	6

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

Gnomad4 AFR exome AF: 0.734

Gnomad4 AMR exome AF: 0.700

Gnomad4 ASJ exome AF: 0.618

Gnomad4 EAS exome AF: 0.872

Gnomad4 SAS exome AF: 0.842

Gnomad4 FIN exome AF: 0.742

Gnomad4 NFE exome AF: 0.648

Gnomad4 OTH exome AF: 0.669

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

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.714

Alfa AF: 0.677 Hom.: 78552

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4785763; hg19: chr16-90066936;