rs11603023

chr11-118615352-T-C

Variant summary

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

The NM_001144758.3(PHLDB1):c.184+670T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,808 control chromosomes in the GnomAD database, including 25,308 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 0.58 (25308 hom., cov: 31)
• Consequence: PHLDB1 NM_001144758.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

Genes affected

PHLDB1 (HGNC:23697): (pleckstrin homology like domain family B member 1) Involved in regulation of embryonic development; regulation of epithelial to mesenchymal transition; and regulation of microtubule cytoskeleton organization. Located in basal cortex. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHLDB1	NM_001144758.3	c.184+670T>C		intron_variant		ENST00000600882.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHLDB1	ENST00000600882.6	c.184+670T>C		intron_variant		1	NM_001144758.3

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87274 AN: 151688 Hom.: 25275 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.575 AC: 87360 AN: 151808 Hom.: 25308 Cov.: 31 AF XY: 0.578 AC XY: 42888 AN XY: 74174

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.572

Alfa AF: 0.580 Hom.: 50460

Bravo AF: 0.582

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.43
Dann	Benign	0.71

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: rs11603023; hg19: chr11-118486067;