chr5-156939170-G-A

Variant names:

• chr5-156939170-G-A
• rs7700944
• NM_138379.3:c.844+9246C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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=-0.84).
• 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 rank	MANE	Protein	UniProt
TIMD4	NM_138379.3	c.844+9246C>T		intron_variant	Intron 5 of 8	ENST00000274532.7	NP_612388.2
TIMD4	NM_001146726.2	c.760+10481C>T		intron_variant	Intron 4 of 7		NP_001140198.1
TIMD4	XM_017010021.2	c.679+12342C>T		intron_variant	Intron 3 of 6		XP_016865510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TIMD4	ENST00000274532.7	c.844+9246C>T		intron_variant	Intron 5 of 8	1	NM_138379.3	ENSP00000274532.2
TIMD4	ENST00000407087.4	c.760+10481C>T		intron_variant	Intron 4 of 7	2		ENSP00000385973.3

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

African (AFR) AF: 0.342 AC: 14159 AN: 41448

American (AMR) AF: 0.351 AC: 5359 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 955 AN: 3466

East Asian (EAS) AF: 0.167 AC: 862 AN: 5176

South Asian (SAS) AF: 0.262 AC: 1258 AN: 4806

European-Finnish (FIN) AF: 0.218 AC: 2306 AN: 10588

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16944 AN: 67982

Other (OTH) AF: 0.305 AC: 643 AN: 2108

Alfa AF: 0.265 Hom.: 21734

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
PhyloP100		-0.15
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: rs7700944; hg19: chr5-156366181; COSMIC: COSV50854491; COSMIC: COSV50854491;