chr5-156956411-A-G

Position:

• chr5-156956411-A-G

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TIMD4	NM_138379.3	c.59-1655T>C		intron_variant		ENST00000274532.7	NP_612388.2
TIMD4	NM_001146726.2	c.59-1655T>C		intron_variant			NP_001140198.1
TIMD4	XM_011534694.3	c.59-1655T>C		intron_variant			XP_011532996.1
TIMD4	XM_017010021.2	c.59-1655T>C		intron_variant			XP_016865510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TIMD4	ENST00000274532.7	c.59-1655T>C		intron_variant		1	NM_138379.3	ENSP00000274532	P2
TIMD4	ENST00000407087.4	c.59-1655T>C		intron_variant		2		ENSP00000385973	A2

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

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.655

Alfa AF: 0.642 Hom.: 12709

Bravo AF: 0.645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.48

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

LitVar

Other links and lift over

dbSNP: rs1363232; hg19: chr5-156383422; COSMIC: COSV50854530;