rs815611

chr5-154139206-G-A

Variant summary

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

The ENST00000518497.6(MFAP3):n.430-10660G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFAP3	ENST00000518497.6	n.430-10660G>A		intron_variant, non_coding_transcript_variant		4
MFAP3	ENST00000519325.1	n.321+4290G>A		intron_variant, non_coding_transcript_variant		3
MFAP3	ENST00000519612.5	n.501+4290G>A		intron_variant, non_coding_transcript_variant		4
MFAP3	ENST00000520327.6	n.293-10660G>A		intron_variant, non_coding_transcript_variant		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;