rs1384302006

Variant names:

• chr5-156951736-G-A
• NM_138379.3:c.455C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-156951736-G-A
• chr5-156951736-G-C

Variant summary

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

The NM_138379.3(TIMD4):​c.455C>T​(p.Thr152Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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: 31)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: TIMD4 NM_138379.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

TIMD4 (HGNC:25132): (T cell immunoglobulin and mucin domain containing 4) Predicted to enable phosphatidylserine binding activity. Predicted to act upstream of or within apoptotic cell clearance. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (MetaRNN=0.077367574).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TIMD4	NM_138379.3	c.455C>T	p.Thr152Ile	missense_variant	Exon 3 of 9	ENST00000274532.7	NP_612388.2
TIMD4	NM_001146726.2	c.455C>T	p.Thr152Ile	missense_variant	Exon 3 of 8		NP_001140198.1
TIMD4	XM_017010021.2	c.455C>T	p.Thr152Ile	missense_variant	Exon 3 of 7		XP_016865510.1
TIMD4	XM_011534694.3	c.455C>T	p.Thr152Ile	missense_variant	Exon 3 of 6		XP_011532996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TIMD4	ENST00000274532.7	c.455C>T	p.Thr152Ile	missense_variant	Exon 3 of 9	1	NM_138379.3	ENSP00000274532.2
TIMD4	ENST00000407087.4	c.455C>T	p.Thr152Ile	missense_variant	Exon 3 of 8	2		ENSP00000385973.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461484 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 726998

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: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.8
DANN	Uncertain	0.98
DEOGEN2	Benign	0.15	T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.084	N
LIST_S2	Benign	0.26	T;T
M_CAP	Benign	0.0015	T
MetaRNN	Benign	0.077	T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	1.6	L;L
PrimateAI	Benign	0.24	T
PROVEAN	Uncertain	-2.4	N;N
REVEL	Benign	0.036
Sift	Benign	0.27	T;T
Sift4G	Benign	0.40	T;T
Polyphen		0.012	B;.
Vest4		0.12
MutPred		0.27		Loss of glycosylation at T152 (P = 0.0076);Loss of glycosylation at T152 (P = 0.0076);
MVP		0.12
MPC		0.055
ClinPred		0.082	T
GERP RS		0.67
Varity_R		0.044
gMVP		0.45

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: chr5-156378747;