chr5-156939170-G-A

Position:

• chr5-156939170-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138379.3(TIMD4):​c.844+9246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,054 control chromosomes in the GnomAD database, including 6,276 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 0.28 (6276 hom., cov: 32)
• Consequence: TIMD4 NM_138379.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TIMD4	NM_138379.3	c.844+9246C>T		intron_variant		ENST00000274532.7	NP_612388.2
TIMD4	NM_001146726.2	c.760+10481C>T		intron_variant			NP_001140198.1
TIMD4	XM_017010021.2	c.679+12342C>T		intron_variant			XP_016865510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TIMD4	ENST00000274532.7	c.844+9246C>T		intron_variant		1	NM_138379.3	ENSP00000274532	P2
TIMD4	ENST00000407087.4	c.760+10481C>T		intron_variant		2		ENSP00000385973	A2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42802 AN: 151936 Hom.: 6270 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.282 AC: 42843 AN: 152054 Hom.: 6276 Cov.: 32 AF XY: 0.280 AC XY: 20827 AN XY: 74322

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.305

Alfa AF: 0.265 Hom.: 9521

Bravo AF: 0.299

Asia WGS AF: 0.209 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.75

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: rs7700944; hg19: chr5-156366181; COSMIC: COSV50854491; COSMIC: COSV50854491;