rs2682547

Variant names:

• chr19-43496905-T-C
• rs2682547
• ENST00000599242.1:c.*198A>G

Your query was ambiguous. Multiple possible variants found:

• chr19-43496905-T-C
• chr19-43496905-T-A
• chr19-43496905-T-G

Variant summary

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

The ENST00000599242.1(PHLDB3):​c.*198A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 709,236 control chromosomes in the GnomAD database, including 61,064 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.39 (11946 hom., cov: 32)
  • Exomes 𝑓: 0.41 (49118 hom.)
• Consequence: PHLDB3 ENST00000599242.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 9 publications found

Genes affected

PHLDB3 (HGNC:30499): (pleckstrin homology like domain family B member 3) Enables enzyme binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000599242.1. 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
	PHLDB3	NM_198850.4	MANE Select	c.825+213A>G		intron	N/A	NP_942147.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHLDB3	ENST00000599242.1	TSL:1	c.*198A>G		3_prime_UTR	Exon 6 of 6	ENSP00000471158.1	Q6NSJ2-2
	PHLDB3	ENST00000292140.10	TSL:5 MANE Select	c.825+213A>G		intron	N/A	ENSP00000292140.5	Q6NSJ2-1
	PHLDB3	ENST00000905838.1		c.825+213A>G		intron	N/A	ENSP00000575897.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59718 AN: 151624 Hom.: 11939 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.373

GnomAD4 exome AF: 0.413 AC: 230180 AN: 557504 Hom.: 49118 Cov.: 8 AF XY: 0.413 AC XY: 112028 AN XY: 271408

African (AFR) AF: 0.385 AC: 4927 AN: 12806

American (AMR) AF: 0.284 AC: 2210 AN: 7790

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 3646 AN: 11104

East Asian (EAS) AF: 0.215 AC: 5184 AN: 24066

South Asian (SAS) AF: 0.374 AC: 3077 AN: 8232

European-Finnish (FIN) AF: 0.483 AC: 10172 AN: 21062

Middle Eastern (MID) AF: 0.329 AC: 624 AN: 1898

European-Non Finnish (NFE) AF: 0.428 AC: 190188 AN: 443898

Other (OTH) AF: 0.381 AC: 10152 AN: 26648

GnomAD4 genome AF: 0.394 AC: 59768 AN: 151732 Hom.: 11946 Cov.: 32 AF XY: 0.392 AC XY: 29019 AN XY: 74092

African (AFR) AF: 0.389 AC: 16085 AN: 41374

American (AMR) AF: 0.312 AC: 4748 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1144 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1094 AN: 5166

South Asian (SAS) AF: 0.358 AC: 1723 AN: 4810

European-Finnish (FIN) AF: 0.488 AC: 5087 AN: 10414

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.421 AC: 28634 AN: 67950

Other (OTH) AF: 0.369 AC: 777 AN: 2108

Alfa AF: 0.397 Hom.: 20545

Bravo AF: 0.375

Asia WGS AF: 0.264 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.042
DANN	Benign	0.42
PhyloP100		-1.7
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: rs2682547; hg19: chr19-44001057;