5-156956411-A-G

Variant names:

• chr5-156956411-A-G
• rs1363232
• NM_138379.3:c.59-1655T>C

Variant summary

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

The NM_138379.3(TIMD4):​c.59-1655T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 152,070 control chromosomes in the GnomAD database, including 32,054 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 0.64 (32054 hom., cov: 32)
• Consequence: TIMD4 NM_138379.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 16 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138379.3. 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
	TIMD4	NM_138379.3	MANE Select	c.59-1655T>C		intron	N/A	NP_612388.2	Q96H15-1
	TIMD4	NM_001146726.2		c.59-1655T>C		intron	N/A	NP_001140198.1	Q96H15-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TIMD4	ENST00000274532.7	TSL:1 MANE Select	c.59-1655T>C		intron	N/A	ENSP00000274532.2	Q96H15-1
	TIMD4	ENST00000407087.4	TSL:2	c.59-1655T>C		intron	N/A	ENSP00000385973.3	Q96H15-2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97871 AN: 151952 Hom.: 32026 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.653

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.644 AC: 97950 AN: 152070 Hom.: 32054 Cov.: 32 AF XY: 0.652 AC XY: 48485 AN XY: 74340

African (AFR) AF: 0.539 AC: 22329 AN: 41454

American (AMR) AF: 0.740 AC: 11302 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2253 AN: 3468

East Asian (EAS) AF: 0.860 AC: 4454 AN: 5182

South Asian (SAS) AF: 0.749 AC: 3618 AN: 4832

European-Finnish (FIN) AF: 0.695 AC: 7340 AN: 10564

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.652 AC: 44330 AN: 67968

Other (OTH) AF: 0.655 AC: 1387 AN: 2116

Alfa AF: 0.649 Hom.: 19947

Bravo AF: 0.645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.48
PhyloP100		0.21
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: rs1363232; hg19: chr5-156383422; COSMIC: COSV50854530;