5-154158681-A-G

Position:

• chr5-154158681-A-G

Variant summary

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

The ENST00000518497.6(MFAP3):​n.1319A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,126 control chromosomes in the GnomAD database, including 24,738 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 0.55 (24738 hom., cov: 33)
• Consequence: MFAP3 ENST00000518497.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 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	ENST00000518497.6	n.1319A>G		non_coding_transcript_exon_variant	4/4	4
MFAP3	ENST00000519325.1	n.402+8735A>G		intron_variant, non_coding_transcript_variant		3
MFAP3	ENST00000520327.6	n.374-1795A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84324 AN: 152008 Hom.: 24719 Cov.: 33

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.555 AC: 84391 AN: 152126 Hom.: 24738 Cov.: 33 AF XY: 0.549 AC XY: 40791 AN XY: 74362

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.0375

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.536

Alfa AF: 0.560 Hom.: 32434

Bravo AF: 0.540

Asia WGS AF: 0.332 AC: 1158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7719067; hg19: chr5-153538241;