16-3242874-C-T

Variant names:

• chr16-3242874-C-T
• rs2741918
• NM_000243.3:c.*267G>A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000243.3(MEFV):​c.*267G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 501,962 control chromosomes in the GnomAD database, including 87,421 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.59 (26841 hom., cov: 30)
  • Exomes 𝑓: 0.58 (60580 hom.)
• Consequence: MEFV NM_000243.3 3_prime_UTR
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: 0.0270

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 16-3242874-C-T is Benign according to our data. Variant chr16-3242874-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 224065.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-3242874-C-T is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEFV	NM_000243.3	c.*267G>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000219596.6	NP_000234.1
MEFV	NM_001198536.2	c.*817G>A		3_prime_UTR_variant	Exon 9 of 9		NP_001185465.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEFV	ENST00000219596	c.*267G>A		3_prime_UTR_variant	Exon 10 of 10	1	NM_000243.3	ENSP00000219596.1

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89647 AN: 151578 Hom.: 26799 Cov.: 30

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.576

GnomAD4 exome AF: 0.583 AC: 204090 AN: 350264 Hom.: 60580 Cov.: 3 AF XY: 0.590 AC XY: 109942 AN XY: 186302

Gnomad4 AFR exome AF: 0.661

Gnomad4 AMR exome AF: 0.694

Gnomad4 ASJ exome AF: 0.561

Gnomad4 EAS exome AF: 0.618

Gnomad4 SAS exome AF: 0.710

Gnomad4 FIN exome AF: 0.560

Gnomad4 NFE exome AF: 0.543

Gnomad4 OTH exome AF: 0.574

GnomAD4 genome AF: 0.592 AC: 89750 AN: 151698 Hom.: 26841 Cov.: 30 AF XY: 0.596 AC XY: 44163 AN XY: 74114

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.577

Alfa AF: 0.567 Hom.: 9593

Bravo AF: 0.600

Asia WGS AF: 0.692 AC: 2407 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial Mediterranean fever Benign:3

Jan 25, 2016

Atomic Energy Commission of Syria (AECS)

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: case-control

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Feb 08, 2023

Genome-Nilou Lab

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Acute febrile neutrophilic dermatosis Benign:1

Feb 08, 2023

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Familial Mediterranean fever, autosomal dominant Benign:1

Feb 08, 2023

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2741918; hg19: chr16-3292874;