rs815611

Variant names:

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

Variant summary

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

The ENST00000519325.1(MFAP3):​n.321+4290G>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 ENST00000519325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

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=-0.81).
• 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

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.0379

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.475

Alfa AF: 0.530 Hom.: 44772

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

Splicing

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

Publications

LitVar

Other links and lift over

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