rs1045241

Variant names:

• chr5-119393591-C-A
• rs1045241
• NM_014350.4:c.*210C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-119393591-C-A
• chr5-119393591-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014350.4(TNFAIP8):​c.*210C>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 0.00000251 in 398,514 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000025 (0 hom.)
• Consequence: TNFAIP8 NM_014350.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014350.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFAIP8	NM_014350.4	MANE Select	c.*210C>A		3_prime_UTR	Exon 2 of 2	NP_055165.2
	TNFAIP8	NM_001286814.1		c.*210C>A		3_prime_UTR	Exon 2 of 2	NP_001273743.1
	TNFAIP8	NM_001286813.2		c.*210C>A		3_prime_UTR	Exon 3 of 3	NP_001273742.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFAIP8	ENST00000504771.3	TSL:1 MANE Select	c.*210C>A		3_prime_UTR	Exon 2 of 2	ENSP00000422245.1
	TNFAIP8	ENST00000415806.2	TSL:1	c.*806C>A		3_prime_UTR	Exon 3 of 3	ENSP00000408534.2
	TNFAIP8	ENST00000513374.1	TSL:2	c.*210C>A		3_prime_UTR	Exon 2 of 2	ENSP00000427424.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000251 AC: 1 AN: 398514 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 209458

African (AFR) AF: 0.00 AC: 0 AN: 11532

American (AMR) AF: 0.00 AC: 0 AN: 15848

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12092

East Asian (EAS) AF: 0.00 AC: 0 AN: 26670

South Asian (SAS) AF: 0.0000250 AC: 1 AN: 40014

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22660

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1708

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 245084

Other (OTH) AF: 0.00 AC: 0 AN: 22906

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.7
DANN	Benign	0.54
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1045241; hg19: chr5-118729286;