19-4652245-C-T

Variant names:

• chr19-4652245-C-T
• NM_152362.3:c.376C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_152362.3(TNFAIP8L1):​c.376C>T​(p.Leu126Leu) variant causes a synonymous change. The variant allele was found at a frequency of 0.000000712 in 1,403,932 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: 7.1e-7 (0 hom.)
• Consequence: TNFAIP8L1 NM_152362.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.67

Genes affected

TNFAIP8L1 (HGNC:28279): (TNF alpha induced protein 8 like 1) Enables identical protein binding activity. Predicted to be involved in negative regulation of TOR signaling. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MYDGF (HGNC:16948): (myeloid derived growth factor) The protein encoded by this gene was previously thought to support proliferation of lymphoid cells and was considered an interleukin. However, this activity has not been reproducible and the function of this protein is currently unknown. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFAIP8L1	NM_152362.3	c.376C>T	p.Leu126Leu	synonymous_variant	Exon 2 of 2	ENST00000327473.9	NP_689575.2
TNFAIP8L1	NM_001167942.1	c.376C>T	p.Leu126Leu	synonymous_variant	Exon 2 of 2		NP_001161414.1
TNFAIP8L1	XM_005259487.4	c.376C>T	p.Leu126Leu	synonymous_variant	Exon 2 of 2		XP_005259544.1
TNFAIP8L1	XM_011527680.3	c.376C>T	p.Leu126Leu	synonymous_variant	Exon 2 of 2		XP_011525982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFAIP8L1	ENST00000327473.9	c.376C>T	p.Leu126Leu	synonymous_variant	Exon 2 of 2	1	NM_152362.3	ENSP00000331827.3
TNFAIP8L1	ENST00000536716.1	c.376C>T	p.Leu126Leu	synonymous_variant	Exon 2 of 2	2		ENSP00000444215.1
MYDGF	ENST00000599761.5	c.184+7686G>A		intron_variant	Intron 3 of 3	3		ENSP00000469136.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.12e-7 AC: 1 AN: 1403932 Hom.: 0 Cov.: 31 AF XY: 0.00000144 AC XY: 1 AN XY: 694308

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.21e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	12
DANN	Benign	0.78

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-4652257;