rs11064

Variant names:

• chr5-119393693-A-G
• rs11064
• NM_014350.4:c.*312A>G

Variant summary

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

The NM_014350.4(TNFAIP8):​c.*312A>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 0.247 in 271,980 control chromosomes in the GnomAD database, including 8,658 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 0.27 (5460 hom., cov: 32)
  • Exomes 𝑓: 0.22 (3198 hom.)
• Consequence: TNFAIP8 NM_014350.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634
• Publications: 27 publications found

Genes affected

TNFAIP8 (HGNC:17260): (TNF alpha induced protein 8) Enables cysteine-type endopeptidase inhibitor activity involved in apoptotic process. Involved in positive regulation of apoptotic process. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFAIP8	NM_014350.4	c.*312A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000504771.3	NP_055165.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFAIP8	ENST00000504771.3	c.*312A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_014350.4	ENSP00000422245.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40493 AN: 152060 Hom.: 5457 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.271

GnomAD4 exome AF: 0.222 AC: 26549 AN: 119802 Hom.: 3198 Cov.: 0 AF XY: 0.219 AC XY: 13650 AN XY: 62380

African (AFR) AF: 0.230 AC: 981 AN: 4262

American (AMR) AF: 0.243 AC: 1341 AN: 5508

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 806 AN: 3754

East Asian (EAS) AF: 0.0945 AC: 792 AN: 8384

South Asian (SAS) AF: 0.152 AC: 1736 AN: 11390

European-Finnish (FIN) AF: 0.253 AC: 1185 AN: 4678

Middle Eastern (MID) AF: 0.229 AC: 119 AN: 520

European-Non Finnish (NFE) AF: 0.243 AC: 18104 AN: 74472

Other (OTH) AF: 0.217 AC: 1485 AN: 6834

GnomAD4 genome AF: 0.266 AC: 40504 AN: 152178 Hom.: 5460 Cov.: 32 AF XY: 0.266 AC XY: 19760 AN XY: 74394

African (AFR) AF: 0.266 AC: 11043 AN: 41532

American (AMR) AF: 0.243 AC: 3724 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3472

East Asian (EAS) AF: 0.0991 AC: 514 AN: 5188

South Asian (SAS) AF: 0.194 AC: 934 AN: 4826

European-Finnish (FIN) AF: 0.310 AC: 3271 AN: 10552

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19122 AN: 67998

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.273 Hom.: 8928

Bravo AF: 0.262

Asia WGS AF: 0.149 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.72
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11064; hg19: chr5-118729388; COSMIC: COSV57226459; COSMIC: COSV57226459;