5-154130036-T-C

Variant names:

• chr5-154130036-T-C
• rs2033195
• ENST00000518497.6:n.429+8139T>C

Variant summary

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

The ENST00000519325.1(MFAP3):​n.250-4809T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,010 control chromosomes in the GnomAD database, including 20,248 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 0.50 (20248 hom., cov: 32)
• Consequence: MFAP3 ENST00000519325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519325.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFAP3	ENST00000518497.6	TSL:4	n.429+8139T>C		intron	N/A
	MFAP3	ENST00000519325.1	TSL:3	n.250-4809T>C		intron	N/A
	MFAP3	ENST00000519612.5	TSL:4	n.430-4809T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76092 AN: 151892 Hom.: 20224 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.501 AC: 76178 AN: 152010 Hom.: 20248 Cov.: 32 AF XY: 0.507 AC XY: 37652 AN XY: 74292

African (AFR) AF: 0.550 AC: 22784 AN: 41414

American (AMR) AF: 0.625 AC: 9540 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1800 AN: 3472

East Asian (EAS) AF: 0.962 AC: 4990 AN: 5188

South Asian (SAS) AF: 0.507 AC: 2447 AN: 4822

European-Finnish (FIN) AF: 0.426 AC: 4495 AN: 10560

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28703 AN: 67960

Other (OTH) AF: 0.512 AC: 1084 AN: 2116

Alfa AF: 0.464 Hom.: 32603

Bravo AF: 0.523

Asia WGS AF: 0.693 AC: 2406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.66
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2033195; hg19: chr5-153509596;