rs707184

Positions:

• chr5-154106266-T-C

Variant summary

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

The ENST00000518497.6(MFAP3):​n.249+8995T>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 0.371 in 151,996 control chromosomes in the GnomAD database, including 10,822 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 0.37 (10822 hom., cov: 32)
• Consequence: MFAP3 ENST00000518497.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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.249+8995T>C		intron_variant, non_coding_transcript_variant		4
MFAP3	ENST00000519325.1	n.249+8995T>C		intron_variant, non_coding_transcript_variant		3
MFAP3	ENST00000519612.5	n.249+8995T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56309 AN: 151878 Hom.: 10811 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.371 AC: 56338 AN: 151996 Hom.: 10822 Cov.: 32 AF XY: 0.367 AC XY: 27274 AN XY: 74284

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.403

Alfa AF: 0.362 Hom.: 1640

Bravo AF: 0.370

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs707184; hg19: chr5-153485826;