chr16-3255732-T-C

Position:

• chr16-3255732-T-C

Variant summary

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

The NM_000243.3(MEFV):​c.277+579A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,900 control chromosomes in the GnomAD database, including 22,364 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 0.53 (22364 hom., cov: 31)
• Consequence: MEFV NM_000243.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

Genes affected

MEFV (HGNC:6998): (MEFV innate immunity regulator, pyrin) This gene encodes a protein, also known as pyrin or marenostrin, that is an important modulator of innate immunity. Mutations in this gene are associated with Mediterranean fever, a hereditary periodic fever syndrome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MEFV	NM_000243.3	c.277+579A>G		intron_variant		ENST00000219596.6	NP_000234.1
MEFV	NM_001198536.2	c.277+579A>G		intron_variant			NP_001185465.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEFV	ENST00000219596.6	c.277+579A>G		intron_variant		1	NM_000243.3	ENSP00000219596	P3

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79650 AN: 151782 Hom.: 22325 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.525 AC: 79749 AN: 151900 Hom.: 22364 Cov.: 31 AF XY: 0.520 AC XY: 38598 AN XY: 74226

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.501

Alfa AF: 0.519 Hom.: 4726

Bravo AF: 0.542

Asia WGS AF: 0.239 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs224226; hg19: chr16-3305732;