5-154130036-T-C

Variant summary

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

The ENST00000518497.6(MFAP3):n.429+8139T>C 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 0.501 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 ENST00000518497.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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 (EAS) allele frequency at 95% confidence interval = 0.94 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.429+8139T>C		intron_variant, non_coding_transcript_variant		4
MFAP3	ENST00000519325.1	n.250-4809T>C		intron_variant, non_coding_transcript_variant		3
MFAP3	ENST00000519612.5	n.430-4809T>C		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.512

Alfa AF: 0.454 Hom.: 21054

Bravo AF: 0.523

Asia WGS AF: 0.693 AC: 2406 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	0.66
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2033195; hg19: chr5-153509596;