rs7125115

chr11-118607615-G-Achr11-118607615-G-C

Variant summary

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

The NM_001144758.3(PHLDB1):c.-106G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 144,560 control chromosomes in the GnomAD database, including 13,259 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 0.41 (13254 hom., cov: 23)
  • Exomes 𝑓: 0.16 (5 hom.)
• Consequence: PHLDB1 NM_001144758.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

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]

LOC124902765 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHLDB1	NM_001144758.3	c.-106G>A		5_prime_UTR_variant	1/23	ENST00000600882.6
LOC124902765	XR_007062908.1	n.390-427C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHLDB1	ENST00000600882.6	c.-106G>A		5_prime_UTR_variant	1/23	1	NM_001144758.3

Frequencies

GnomAD3 genomes AF: 0.411 AC: 59312 AN: 144238 Hom.: 13234 Cov.: 23

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.432

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.406

GnomAD4 exome AF: 0.160 AC: 34 AN: 212 Hom.: 5 Cov.: 0 AF XY: 0.141 AC XY: 20 AN XY: 142

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.167

Gnomad4 EAS exome AF: 0.0625

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.155

Gnomad4 OTH exome AF: 0.0714

GnomAD4 genome AF: 0.411 AC: 59363 AN: 144348 Hom.: 13254 Cov.: 23 AF XY: 0.408 AC XY: 28543 AN XY: 70006

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.410

Alfa AF: 0.378 Hom.: 3712

Bravo AF: 0.429

Asia WGS AF: 0.433 AC: 1495 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	15
Dann	Benign	0.76

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: rs7125115; hg19: chr11-118478330;