rs7715256

chr5-154158333-G-T

Variant summary

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

The ENST00000518497.6(MFAP3):n.971G>T 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 0.545 in 151,960 control chromosomes in the GnomAD database, including 23,730 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 0.54 (23730 hom., cov: 32)
• Consequence: MFAP3 ENST00000518497.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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.971G>T		non_coding_transcript_exon_variant	4/4	4
MFAP3	ENST00000519325.1	n.402+8387G>T		intron_variant, non_coding_transcript_variant		3
MFAP3	ENST00000520327.6	n.374-2143G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82757 AN: 151842 Hom.: 23716 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.545 AC: 82816 AN: 151960 Hom.: 23730 Cov.: 32 AF XY: 0.540 AC XY: 40088 AN XY: 74286

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.0375

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.524

Alfa AF: 0.568 Hom.: 3631

Bravo AF: 0.528

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.20
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7715256; hg19: chr5-153537893;