10-110079115-G-C

Variant names:

• chr10-110079115-G-C
• rs2501578
• NM_016824.5:c.-29-21510G>C

Variant summary

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

The NM_016824.5(ADD3):​c.-29-21510G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,860 control chromosomes in the GnomAD database, including 30,581 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 0.60 (30581 hom., cov: 30)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ADD3 NM_016824.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

Genes affected

ADD3 (HGNC:245): (adducin 3) Adducins are heteromeric proteins composed of different subunits referred to as adducin alpha, beta and gamma. The three subunits are encoded by distinct genes and belong to a family of membrane skeletal proteins involved in the assembly of spectrin-actin network in erythrocytes and at sites of cell-cell contact in epithelial tissues. While adducins alpha and gamma are ubiquitously expressed, the expression of adducin beta is restricted to brain and hematopoietic tissues. Adducin, originally purified from human erythrocytes, was found to be a heterodimer of adducins alpha and beta. Polymorphisms resulting in amino acid substitutions in these two subunits have been associated with the regulation of blood pressure in an animal model of hypertension. Heterodimers consisting of alpha and gamma subunits have also been described. Structurally, each subunit is comprised of two distinct domains. The amino-terminal region is protease resistant and globular in shape, while the carboxy-terminal region is protease sensitive. The latter contains multiple phosphorylation sites for protein kinase C, the binding site for calmodulin, and is required for association with spectrin and actin. Alternatively spliced adducin gamma transcripts encoding different isoforms have been described. The functions of the different isoforms are not known. [provided by RefSeq, Jul 2008]

ADD3 Gene-Disease associations (from GenCC):

• cerebral palsy, spastic quadriplegic, 3

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• complex neurodevelopmental disorder with motor features

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen
• spastic quadriplegic cerebral palsy

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016824.5. 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
	ADD3	NM_016824.5	MANE Select	c.-29-21510G>C		intron	N/A	NP_058432.1
	ADD3	NM_001320591.2		c.-29-21510G>C		intron	N/A	NP_001307520.1
	ADD3	NM_001320592.2		c.-29-21510G>C		intron	N/A	NP_001307521.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADD3	ENST00000356080.9	TSL:1 MANE Select	c.-29-21510G>C		intron	N/A	ENSP00000348381.4
	ADD3	ENST00000277900.12	TSL:1	c.-29-21510G>C		intron	N/A	ENSP00000277900.8
	ADD3	ENST00000360162.7	TSL:1	c.-29-21510G>C		intron	N/A	ENSP00000353286.3

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90518 AN: 151732 Hom.: 30501 Cov.: 30

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.585

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.597 AC: 90665 AN: 151854 Hom.: 30581 Cov.: 30 AF XY: 0.600 AC XY: 44548 AN XY: 74216

African (AFR) AF: 0.894 AC: 37022 AN: 41432

American (AMR) AF: 0.661 AC: 10086 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1844 AN: 3460

East Asian (EAS) AF: 0.776 AC: 4000 AN: 5156

South Asian (SAS) AF: 0.755 AC: 3638 AN: 4816

European-Finnish (FIN) AF: 0.388 AC: 4090 AN: 10530

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28176 AN: 67896

Other (OTH) AF: 0.590 AC: 1242 AN: 2104

Alfa AF: 0.509 Hom.: 2800

Bravo AF: 0.627

Asia WGS AF: 0.806 AC: 2791 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.26
DANN	Benign	0.48
PhyloP100		-1.5
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: rs2501578; hg19: chr10-111838873;