5-154163906-A-G

Position:

• chr5-154163906-A-G

Variant summary

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

The ENST00000519325.1(MFAP3):​n.402+13960A>G 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 0.569 in 152,236 control chromosomes in the GnomAD database, including 26,230 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 0.57 (26230 hom., cov: 34)
• Consequence: MFAP3 ENST00000519325.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MFAP3	ENST00000519325.1	n.402+13960A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86581 AN: 152118 Hom.: 26202 Cov.: 34

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.569 AC: 86661 AN: 152236 Hom.: 26230 Cov.: 34 AF XY: 0.563 AC XY: 41910 AN XY: 74442

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.0372

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.548

Alfa AF: 0.531 Hom.: 3776

Bravo AF: 0.556

Asia WGS AF: 0.338 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0090
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7708584; hg19: chr5-153543466;