ENST00000519325.1:n.402+13960A>G

Variant names:

• chr5-154163906-A-G
• rs7708584
• ENST00000519325.1:n.402+13960A>G

Variant summary

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

The ENST00000519325.1(MFAP3):​n.402+13960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,236 control chromosomes in the GnomAD database, including 26,230 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 0.57 (26230 hom., cov: 34)
• Consequence: MFAP3 ENST00000519325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 23 publications found

Genes affected

MFAP3 (HGNC:7034): (microfibril associated protein 3) Predicted to be located in extracellular region. Predicted to be active in cytoplasm; nucleus; and plasma membrane. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFAP3	ENST00000519325.1	n.402+13960A>G		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86581 AN: 152118 Hom.: 26202 Cov.: 34

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.569 AC: 86661 AN: 152236 Hom.: 26230 Cov.: 34 AF XY: 0.563 AC XY: 41910 AN XY: 74442

African (AFR) AF: 0.700 AC: 29059 AN: 41528

American (AMR) AF: 0.394 AC: 6027 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1673 AN: 3472

East Asian (EAS) AF: 0.0372 AC: 193 AN: 5184

South Asian (SAS) AF: 0.515 AC: 2485 AN: 4826

European-Finnish (FIN) AF: 0.594 AC: 6296 AN: 10600

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38897 AN: 68014

Other (OTH) AF: 0.548 AC: 1158 AN: 2114

Alfa AF: 0.561 Hom.: 37681

Bravo AF: 0.556

Asia WGS AF: 0.338 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0090
DANN	Benign	0.21
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7708584; hg19: chr5-153543466;