rs16900627

Variant names:

• chr8-89790767-A-G
• rs16900627
• NM_003821.6:c.*351A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003821.6(RIPK2):​c.*351A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 193,952 control chromosomes in the GnomAD database, including 3,805 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.17 (3580 hom., cov: 32)
  • Exomes 𝑓: 0.081 (225 hom.)
• Consequence: RIPK2 NM_003821.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 15 publications found

Genes affected

RIPK2 (HGNC:10020): (receptor interacting serine/threonine kinase 2) This gene encodes a member of the receptor-interacting protein (RIP) family of serine/threonine protein kinases. The encoded protein contains a C-terminal caspase activation and recruitment domain (CARD), and is a component of signaling complexes in both the innate and adaptive immune pathways. It is a potent activator of NF-kappaB and inducer of apoptosis in response to various stimuli. [provided by RefSeq, Jul 2008]

PARAIL (HGNC:55545): (palmitic acid regulated anti-inflammatory lncRNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003821.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPK2	NM_003821.6	MANE Select	c.*351A>G		3_prime_UTR	Exon 11 of 11	NP_003812.1
	RIPK2	NM_001375360.1		c.*351A>G		3_prime_UTR	Exon 10 of 10	NP_001362289.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIPK2	ENST00000220751.5	TSL:1 MANE Select	c.*351A>G		3_prime_UTR	Exon 11 of 11	ENSP00000220751.4
	RIPK2	ENST00000929530.1		c.*351A>G		3_prime_UTR	Exon 12 of 12	ENSP00000599589.1
	RIPK2	ENST00000893222.1		c.*351A>G		3_prime_UTR	Exon 10 of 10	ENSP00000563281.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25316 AN: 151944 Hom.: 3560 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0615

Gnomad FIN AF: 0.0766

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.0809 AC: 3389 AN: 41890 Hom.: 225 Cov.: 0 AF XY: 0.0803 AC XY: 1792 AN XY: 22312

African (AFR) AF: 0.391 AC: 248 AN: 634

American (AMR) AF: 0.0793 AC: 256 AN: 3230

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 111 AN: 908

East Asian (EAS) AF: 0.134 AC: 287 AN: 2136

South Asian (SAS) AF: 0.0556 AC: 285 AN: 5126

European-Finnish (FIN) AF: 0.0789 AC: 127 AN: 1610

Middle Eastern (MID) AF: 0.133 AC: 16 AN: 120

European-Non Finnish (NFE) AF: 0.0710 AC: 1846 AN: 25994

Other (OTH) AF: 0.0999 AC: 213 AN: 2132

GnomAD4 genome AF: 0.167 AC: 25373 AN: 152062 Hom.: 3580 Cov.: 32 AF XY: 0.163 AC XY: 12148 AN XY: 74356

African (AFR) AF: 0.388 AC: 16088 AN: 41430

American (AMR) AF: 0.0971 AC: 1483 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 366 AN: 3466

East Asian (EAS) AF: 0.158 AC: 817 AN: 5180

South Asian (SAS) AF: 0.0623 AC: 301 AN: 4828

European-Finnish (FIN) AF: 0.0766 AC: 811 AN: 10592

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.0753 AC: 5120 AN: 67972

Other (OTH) AF: 0.151 AC: 318 AN: 2110

Alfa AF: 0.102 Hom.: 1632

Bravo AF: 0.182

Asia WGS AF: 0.110 AC: 383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.9
DANN	Benign	0.75
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16900627; hg19: chr8-90802995;