rs7715256

Variant names:

• chr5-154158333-G-T
• rs7715256
• ENST00000518497.6:n.971G>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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFAP3	ENST00000518497.6	n.971G>T		non_coding_transcript_exon_variant	Exon 4 of 4	4
MFAP3	ENST00000519325.1	n.402+8387G>T		intron_variant	Intron 3 of 4	3
MFAP3	ENST00000520327.6	n.374-2143G>T		intron_variant	Intron 3 of 3	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;