ENST00000361417.6:c.-199A>G

Variant names:

• chr11-118606652-A-G
• rs498872
• ENST00000361417.6:c.-199A>G

Variant summary

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

The ENST00000361417.6(PHLDB1):​c.-199A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,186 control chromosomes in the GnomAD database, including 43,132 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 0.75 (43102 hom., cov: 31)
  • Exomes 𝑓: 0.77 (30 hom.)
• Consequence: PHLDB1 ENST00000361417.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64
• Publications: 99 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361417.6. 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
	PHLDB1	NM_015157.4		c.-199A>G		5_prime_UTR	Exon 1 of 24	NP_055972.1	Q86UU1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHLDB1	ENST00000361417.6	TSL:1	c.-199A>G		5_prime_UTR	Exon 1 of 24	ENSP00000354498.2	Q86UU1-1
	PHLDB1	ENST00000860943.1		c.-42A>G		5_prime_UTR	Exon 1 of 22	ENSP00000531002.1
	PHLDB1	ENST00000860941.1		c.-42A>G		5_prime_UTR	Exon 1 of 21	ENSP00000531000.1

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113646 AN: 151964 Hom.: 43050 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.746

GnomAD4 exome AF: 0.769 AC: 80 AN: 104 Hom.: 30 Cov.: 0 AF XY: 0.782 AC XY: 61 AN XY: 78

African (AFR) AF: 0.875 AC: 7 AN: 8

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.600 AC: 6 AN: 10

Middle Eastern (MID) AF: 1.00 AC: 4 AN: 4

European-Non Finnish (NFE) AF: 0.788 AC: 52 AN: 66

Other (OTH) AF: 0.667 AC: 8 AN: 12

GnomAD4 genome AF: 0.748 AC: 113756 AN: 152082 Hom.: 43102 Cov.: 31 AF XY: 0.745 AC XY: 55344 AN XY: 74320

African (AFR) AF: 0.886 AC: 36772 AN: 41500

American (AMR) AF: 0.732 AC: 11185 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2632 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3819 AN: 5172

South Asian (SAS) AF: 0.631 AC: 3039 AN: 4818

European-Finnish (FIN) AF: 0.668 AC: 7050 AN: 10552

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46754 AN: 67968

Other (OTH) AF: 0.747 AC: 1578 AN: 2112

Alfa AF: 0.713 Hom.: 154622

Bravo AF: 0.765

Asia WGS AF: 0.712 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	16
DANN	Benign	0.74
PhyloP100		1.6
PromoterAI		-0.041	Neutral
Mutation Taster		=297/3	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs498872; hg19: chr11-118477367;