chr5-154139206-G-A

Variant names:

• chr5-154139206-G-A
• rs815611
• ENST00000518497.6:n.430-10660G>A

Variant summary

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

The ENST00000518497.6(MFAP3):​n.430-10660G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,992 control chromosomes in the GnomAD database, including 18,638 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 0.48 (18638 hom., cov: 31)
• Consequence: MFAP3 ENST00000518497.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 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.430-10660G>A		intron_variant	Intron 2 of 3	4
MFAP3	ENST00000519325.1	n.321+4290G>A		intron_variant	Intron 2 of 4	3
MFAP3	ENST00000519612.5	n.501+4290G>A		intron_variant	Intron 3 of 3	4
MFAP3	ENST00000520327.6	n.293-10660G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73051 AN: 151872 Hom.: 18640 Cov.: 31

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.0378

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.481 AC: 73087 AN: 151992 Hom.: 18638 Cov.: 31 AF XY: 0.477 AC XY: 35439 AN XY: 74288

African (AFR) AF: 0.438 AC: 18167 AN: 41438

American (AMR) AF: 0.359 AC: 5480 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1649 AN: 3470

East Asian (EAS) AF: 0.0379 AC: 196 AN: 5178

South Asian (SAS) AF: 0.472 AC: 2271 AN: 4810

European-Finnish (FIN) AF: 0.568 AC: 6007 AN: 10576

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37454 AN: 67932

Other (OTH) AF: 0.475 AC: 1003 AN: 2112

Alfa AF: 0.524 Hom.: 92252

Bravo AF: 0.460

Asia WGS AF: 0.295 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.72
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs815611; hg19: chr5-153518766; COSMIC: COSV72801518;