5-169787-T-C

Variant names:

• chr5-169787-T-C
• rs1108867
• NM_052909.5:c.3729+195T>C

Variant summary

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

The NM_052909.5(PLEKHG4B):​c.3729+195T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,190 control chromosomes in the GnomAD database, including 34,045 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 0.66 (34045 hom., cov: 34)
• Consequence: PLEKHG4B NM_052909.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 2 publications found

Genes affected

PLEKHG4B (HGNC:29399): (pleckstrin homology and RhoGEF domain containing G4B) This gene encodes a large protein that contains a pleckstrin homology domain and may function as a guanine nucleotide exchange factor. [provided by RefSeq, May 2017]

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 (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052909.5. 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
	PLEKHG4B	NM_052909.5	MANE Select	c.3729+195T>C		intron	N/A	NP_443141.4	Q96PX9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLEKHG4B	ENST00000637938.2	TSL:5 MANE Select	c.3729+195T>C		intron	N/A	ENSP00000490806.1	Q96PX9
	PLEKHG4B	ENST00000283426.11	TSL:1	c.2661+195T>C		intron	N/A	ENSP00000283426.6	A0AAK2PKJ8
	PLEKHG4B	ENST00000924300.1		c.3726+195T>C		intron	N/A	ENSP00000594359.1

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100674 AN: 152072 Hom.: 34021 Cov.: 34

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.662 AC: 100756 AN: 152190 Hom.: 34045 Cov.: 34 AF XY: 0.656 AC XY: 48796 AN XY: 74418

African (AFR) AF: 0.648 AC: 26922 AN: 41524

American (AMR) AF: 0.567 AC: 8670 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2149 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1444 AN: 5156

South Asian (SAS) AF: 0.620 AC: 2992 AN: 4828

European-Finnish (FIN) AF: 0.681 AC: 7219 AN: 10602

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.722 AC: 49122 AN: 68008

Other (OTH) AF: 0.639 AC: 1350 AN: 2114

Alfa AF: 0.695 Hom.: 27665

Bravo AF: 0.648

Asia WGS AF: 0.440 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		-0.59
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: rs1108867; hg19: chr5-169902; COSMIC: COSV52055222;