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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901118	XR_007059010.1	n.84+4116A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFAP3	ENST00000519325.1	n.403-32149T>C		intron_variant	Intron 3 of 4	3
ENSG00000299992	ENST00000767861.1	n.433+4116A>G		intron_variant	Intron 1 of 1
ENSG00000300013	ENST00000767947.1	n.*13T>C		downstream_gene_variant

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 v4.3

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

Other links and lift over

dbSNP: rs1078703; hg19: chr5-153565440;