rs7125115

Variant names:

• chr11-118607615-G-A
• rs7125115
• NM_001144758.3:c.-106G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-118607615-G-A
• chr11-118607615-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 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=-0.67).
• 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 rank	MANE	Protein	UniProt
PHLDB1	NM_001144758.3	c.-106G>A		5_prime_UTR_variant	Exon 1 of 23	ENST00000600882.6	NP_001138230.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHLDB1	ENST00000600882.6	c.-106G>A		5_prime_UTR_variant	Exon 1 of 23	1	NM_001144758.3	ENSP00000469820.1

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

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AF: 0.167 AC: 1 AN: 6

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.0625 AC: 1 AN: 16

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

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.155 AC: 26 AN: 168

Other (OTH) AF: 0.0714 AC: 1 AN: 14

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

African (AFR) AF: 0.589 AC: 22244 AN: 37786

American (AMR) AF: 0.286 AC: 4182 AN: 14638

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1353 AN: 3428

East Asian (EAS) AF: 0.303 AC: 1455 AN: 4808

South Asian (SAS) AF: 0.458 AC: 2064 AN: 4510

European-Finnish (FIN) AF: 0.287 AC: 2644 AN: 9220

Middle Eastern (MID) AF: 0.421 AC: 117 AN: 278

European-Non Finnish (NFE) AF: 0.363 AC: 24213 AN: 66780

Other (OTH) AF: 0.410 AC: 823 AN: 2008

Alfa AF: 0.383 Hom.: 4696

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
PhyloP100		-0.057
PromoterAI		0.15	Neutral
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: rs7125115; hg19: chr11-118478330;