rs273506

Variant names:

• chr19-18110837-C-A
• rs273506
• NM_001393504.1:c.161+96C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-18110837-C-A
• chr19-18110837-C-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001393504.1(MAST3):​c.161+96C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000576 in 520,660 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000059 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000057 (0 hom.)
• Consequence: MAST3 NM_001393504.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 8 publications found

Genes affected

MAST3 (HGNC:19036): (microtubule associated serine/threonine kinase 3) Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in cytoskeleton organization; intracellular signal transduction; and peptidyl-serine phosphorylation. [provided by Alliance of Genome Resources, Apr 2022]

MAST3 Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy 108

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAST3	NM_001393504.1	c.161+96C>A		intron_variant	Intron 3 of 27	ENST00000687212.1	NP_001380433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAST3	ENST00000687212.1	c.161+96C>A		intron_variant	Intron 3 of 27		NM_001393504.1	ENSP00000509890.1

Frequencies

GnomAD3 genomes AF: 0.0000592 AC: 9 AN: 151992 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000262

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000736

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000570 AC: 21 AN: 368668 Hom.: 0 AF XY: 0.0000576 AC XY: 10 AN XY: 173714

African (AFR) AF: 0.000152 AC: 1 AN: 6560

American (AMR) AF: 0.00 AC: 0 AN: 392

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2282

East Asian (EAS) AF: 0.00 AC: 0 AN: 1514

South Asian (SAS) AF: 0.00 AC: 0 AN: 7318

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 558

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 722

European-Non Finnish (NFE) AF: 0.0000593 AC: 20 AN: 337172

Other (OTH) AF: 0.00 AC: 0 AN: 12150

GnomAD4 genome AF: 0.0000592 AC: 9 AN: 151992 Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 5 AN XY: 74218

African (AFR) AF: 0.00 AC: 0 AN: 41364

American (AMR) AF: 0.000262 AC: 4 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10576

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.0000736 AC: 5 AN: 67978

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.00 Hom.: 42478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.71
PhyloP100		-0.28

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: rs273506; hg19: chr19-18221647;