chr5-154158681-A-G

Variant names:

• chr5-154158681-A-G
• rs7719067
• ENST00000518497.6:n.1319A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFAP3	ENST00000518497.6	n.1319A>G		non_coding_transcript_exon_variant	Exon 4 of 4	4
MFAP3	ENST00000519325.1	n.402+8735A>G		intron_variant	Intron 3 of 4	3
MFAP3	ENST00000520327.6	n.374-1795A>G		intron_variant	Intron 3 of 3	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

African (AFR) AF: 0.650 AC: 26959 AN: 41478

American (AMR) AF: 0.387 AC: 5912 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3470

East Asian (EAS) AF: 0.0375 AC: 194 AN: 5180

South Asian (SAS) AF: 0.514 AC: 2479 AN: 4822

European-Finnish (FIN) AF: 0.595 AC: 6289 AN: 10576

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38884 AN: 67994

Other (OTH) AF: 0.536 AC: 1133 AN: 2112

Alfa AF: 0.556 Hom.: 44834

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
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs7719067; hg19: chr5-153538241;