rs1078703

Variant names:

• chr5-154185880-T-C
• rs1078703
• ENST00000519325.1:n.403-32149T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-154185880-T-C
• chr5-154185880-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519325.1(MFAP3):​n.403-32149T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,020 control chromosomes in the GnomAD database, including 24,558 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 0.55 (24558 hom., cov: 32)
• Consequence: MFAP3 ENST00000519325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 1 publications found

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]

ENSG00000299992 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519325.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFAP3	ENST00000519325.1	TSL:3	n.403-32149T>C		intron	N/A
	ENSG00000299992	ENST00000767861.1		n.433+4116A>G		intron	N/A
	ENSG00000300013	ENST00000767947.1		n.*13T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83765 AN: 151900 Hom.: 24543 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.0800

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.551 AC: 83823 AN: 152020 Hom.: 24558 Cov.: 32 AF XY: 0.546 AC XY: 40559 AN XY: 74306

African (AFR) AF: 0.704 AC: 29183 AN: 41444

American (AMR) AF: 0.393 AC: 6002 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1676 AN: 3472

East Asian (EAS) AF: 0.0798 AC: 412 AN: 5166

South Asian (SAS) AF: 0.415 AC: 1997 AN: 4808

European-Finnish (FIN) AF: 0.605 AC: 6385 AN: 10556

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36190 AN: 67980

Other (OTH) AF: 0.536 AC: 1130 AN: 2110

Alfa AF: 0.514 Hom.: 3852

Bravo AF: 0.541

Asia WGS AF: 0.322 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0030
DANN	Benign	0.21
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1078703;

hg19: chr5-153565440;