5-154065390-A-G

Position:

• chr5-154065390-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521527.5(MFAP3):​n.38+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 ENST00000521527.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MFAP3	ENST00000520327.6	n.44+26379A>G		intron_variant		5
MFAP3	ENST00000521527.5	n.38+26379A>G		intron_variant		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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.620

Alfa AF: 0.653 Hom.: 5166

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1438588; hg19: chr5-153444950;