chr19-53793687-C-A

Position:

• chr19-53793687-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001277129.1(NLRP12):​c.*362G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0033 in 329,694 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0031 (5 hom., cov: 27)
  • Exomes 𝑓: 0.0035 (6 hom.)
• Consequence: NLRP12 NM_001277129.1 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.935

Genes affected

NLRP12 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 19-53793687-C-A is Benign according to our data. Variant chr19-53793687-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 329986.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NLRP12	NM_001277129.1	c.*362G>T		3_prime_UTR_variant	9/9		NP_001264058.1
NLRP12	XM_011527479.2	c.*362G>T		3_prime_UTR_variant	9/9		XP_011525781.1
NLRP12	XM_011527480.2	c.*362G>T		3_prime_UTR_variant	9/9		XP_011525782.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00310 AC: 465 AN: 149922 Hom.: 5 Cov.: 27

Gnomad AFR AF: 0.000516

Gnomad AMI AF: 0.00332

Gnomad AMR AF: 0.00411

Gnomad ASJ AF: 0.00290

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00287

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00495

Gnomad OTH AF: 0.00290

GnomAD4 exome AF: 0.00347 AC: 623 AN: 179656 Hom.: 6 Cov.: 0 AF XY: 0.00289 AC XY: 280 AN XY: 96868

Gnomad4 AFR exome AF: 0.000178

Gnomad4 AMR exome AF: 0.00156

Gnomad4 ASJ exome AF: 0.00159

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000191

Gnomad4 FIN exome AF: 0.00291

Gnomad4 NFE exome AF: 0.00528

Gnomad4 OTH exome AF: 0.00337

GnomAD4 genome AF: 0.00309 AC: 464 AN: 150038 Hom.: 5 Cov.: 27 AF XY: 0.00300 AC XY: 219 AN XY: 73112

Gnomad4 AFR AF: 0.000514

Gnomad4 AMR AF: 0.00411

Gnomad4 ASJ AF: 0.00290

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00287

Gnomad4 NFE AF: 0.00494

Gnomad4 OTH AF: 0.00287

Alfa AF: 0.00197 Hom.: 1

Bravo AF: 0.00301

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial cold autoinflammatory syndrome 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

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.80

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: rs562576939; hg19: chr19-54296941;