6-150804115-G-T

Variant names:

• chr6-150804115-G-T
• rs10046456
• NM_001029884.3:c.781-495G>T

Variant summary

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

The NM_001029884.3(PLEKHG1):​c.781-495G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.10 (973 hom., cov: 20)
• Consequence: PLEKHG1 NM_001029884.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

Genes affected

PLEKHG1 (HGNC:20884): (pleckstrin homology and RhoGEF domain containing G1) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Located in nucleoplasm. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLEKHG1	NM_001029884.3	c.781-495G>T		intron_variant	Intron 7 of 16	ENST00000696526.1	NP_001025055.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLEKHG1	ENST00000696526.1	c.781-495G>T		intron_variant	Intron 7 of 16		NM_001029884.3	ENSP00000512689.1
PLEKHG1	ENST00000475490.1	n.322-495G>T		intron_variant	Intron 4 of 14	1		ENSP00000433107.1
PLEKHG1	ENST00000358517.6	c.781-495G>T		intron_variant	Intron 6 of 15	5		ENSP00000351318.2
PLEKHG1	ENST00000644968.1	c.781-495G>T		intron_variant	Intron 6 of 15			ENSP00000496254.1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 12357 AN: 123392 Hom.: 976 Cov.: 20

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00118

Gnomad AMR AF: 0.0524

Gnomad ASJ AF: 0.0750

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0333

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0919

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

GnomAD4 genome AF: 0.100 AC: 12344 AN: 123420 Hom.: 973 Cov.: 20 AF XY: 0.104 AC XY: 6054 AN XY: 57978

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0523

Gnomad4 ASJ AF: 0.0750

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0562

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0556 Hom.: 404

Asia WGS AF: 0.148 AC: 510 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.27

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: rs10046456; hg19: chr6-151125251;