2-205442824-G-A

Variant names:

• chr2-205442824-G-A
• rs11896375
• NM_001302769.2:c.3044+2152G>A

Variant summary

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

The NM_001302769.2(PARD3B):​c.3044+2152G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,100 control chromosomes in the GnomAD database, including 1,102 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 0.10 (1102 hom., cov: 32)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 2 publications found

Genes affected

PARD3B (HGNC:14446): (par-3 family cell polarity regulator beta) Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in several processes, including establishment of cell polarity; establishment of centrosome localization; and establishment or maintenance of epithelial cell apical/basal polarity. Located in cell junction. Part of protein-containing complex. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001302769.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3B	NM_001302769.2	MANE Select	c.3044+2152G>A		intron	N/A	NP_001289698.1
	PARD3B	NM_152526.6		c.2858+2152G>A		intron	N/A	NP_689739.4
	PARD3B	NM_057177.7		c.2837+2152G>A		intron	N/A	NP_476518.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3B	ENST00000406610.7	TSL:1 MANE Select	c.3044+2152G>A		intron	N/A	ENSP00000385848.2
	PARD3B	ENST00000358768.6	TSL:1	c.2858+2152G>A		intron	N/A	ENSP00000351618.2
	PARD3B	ENST00000351153.5	TSL:1	c.2837+2152G>A		intron	N/A	ENSP00000317261.2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15287 AN: 151982 Hom.: 1099 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.101 AC: 15310 AN: 152100 Hom.: 1102 Cov.: 32 AF XY: 0.0958 AC XY: 7125 AN XY: 74358

African (AFR) AF: 0.205 AC: 8502 AN: 41444

American (AMR) AF: 0.0796 AC: 1217 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0189 AC: 91 AN: 4820

European-Finnish (FIN) AF: 0.0457 AC: 484 AN: 10588

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0651 AC: 4429 AN: 67998

Other (OTH) AF: 0.0942 AC: 199 AN: 2112

Alfa AF: 0.0811 Hom.: 133

Bravo AF: 0.108

Asia WGS AF: 0.0250 AC: 86 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.81
PhyloP100		-0.087
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: rs11896375; hg19: chr2-206307548;