rs707184

Variant names:

• chr5-154106266-T-C
• rs707184
• ENST00000518497.6:n.249+8995T>C

Variant summary

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

The ENST00000519325.1(MFAP3):​n.249+8995T>C variant causes a intron 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 ENST00000519325.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFAP3	ENST00000518497.6	n.249+8995T>C		intron_variant	Intron 1 of 3	4
MFAP3	ENST00000519325.1	n.249+8995T>C		intron_variant	Intron 1 of 4	3
MFAP3	ENST00000519612.5	n.249+8995T>C		intron_variant	Intron 1 of 3	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;