chr16-3242304-C-CAGT

Position:

• chr16-3242304-C-CAGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000243.3(MEFV):​c.*836_*837insACT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.59 (26119 hom., cov: 0)
  • Exomes 𝑓: 0.58 (1257 hom.)
• Consequence: MEFV NM_000243.3 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.355

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 -10 ACMG points.

• BP6: Variant 16-3242304-C-CAGT is Benign according to our data. Variant chr16-3242304-C-CAGT is described in ClinVar as [Likely_benign]. Clinvar id is 319088.Status of the report is criteria_provided_single_submitter, 1 stars.
• 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/exons	MANE	Protein	UniProt
MEFV	NM_000243.3	c.*836_*837insACT		3_prime_UTR_variant	10/10	ENST00000219596.6	NP_000234.1
MEFV	NM_001198536.2	c.*1386_*1387insACT		3_prime_UTR_variant	9/9		NP_001185465.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MEFV	ENST00000219596	c.*836_*837insACT		3_prime_UTR_variant	10/10	1	NM_000243.3	ENSP00000219596.1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 87059 AN: 146534 Hom.: 26080 Cov.: 0

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.586

GnomAD3 exomes AF: 0.634 AC: 161 AN: 254 Hom.: 52 AF XY: 0.660 AC XY: 99 AN XY: 150

Gnomad AFR exome AF: 1.00

Gnomad AMR exome AF: 0.758

Gnomad ASJ exome AF: 0.500

Gnomad EAS exome AF: 1.00

Gnomad SAS exome AF: 0.735

Gnomad FIN exome AF: 0.500

Gnomad NFE exome AF: 0.474

Gnomad OTH exome AF: 0.500

GnomAD4 exome AF: 0.577 AC: 3787 AN: 6560 Hom.: 1257 Cov.: 0 AF XY: 0.601 AC XY: 2676 AN XY: 4452

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.728

Gnomad4 ASJ exome AF: 0.511

Gnomad4 EAS exome AF: 0.786

Gnomad4 SAS exome AF: 0.675

Gnomad4 FIN exome AF: 0.493

Gnomad4 NFE exome AF: 0.478

Gnomad4 OTH exome AF: 0.431

GnomAD4 genome AF: 0.594 AC: 87157 AN: 146650 Hom.: 26119 Cov.: 0 AF XY: 0.598 AC XY: 42560 AN XY: 71148

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.588

Alfa AF: 0.353 Hom.: 581

Asia WGS AF: 0.692 AC: 2406 AN: 3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial Mediterranean fever Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34895148; hg19: chr16-3292304;