chr5-154065390-A-G

Variant names:

• chr5-154065390-A-G
• rs1438588
• ENST00000520327.6:n.44+26379A>G

Variant summary

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

The ENST00000520327.6(MFAP3):​n.44+26379A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,090 control chromosomes in the GnomAD database, including 32,518 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 0.65 (32518 hom., cov: 32)
• Consequence: MFAP3 ENST00000520327.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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	ENST00000520327.6	n.44+26379A>G		intron_variant	Intron 1 of 3	5
MFAP3	ENST00000521527.5	n.38+26379A>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98759 AN: 151972 Hom.: 32464 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.650 AC: 98865 AN: 152090 Hom.: 32518 Cov.: 32 AF XY: 0.653 AC XY: 48570 AN XY: 74352

African (AFR) AF: 0.650 AC: 26969 AN: 41470

American (AMR) AF: 0.683 AC: 10442 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2103 AN: 3470

East Asian (EAS) AF: 0.877 AC: 4550 AN: 5186

South Asian (SAS) AF: 0.732 AC: 3526 AN: 4816

European-Finnish (FIN) AF: 0.622 AC: 6572 AN: 10564

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.629 AC: 42765 AN: 67978

Other (OTH) AF: 0.620 AC: 1309 AN: 2112

Alfa AF: 0.654 Hom.: 5341

Bravo AF: 0.653

Asia WGS AF: 0.797 AC: 2774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.49
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs1438588; hg19: chr5-153444950;